Surveillance of Phytophthora agathidicida, the causal agent of kauri dieback, has relied on soil baiting and loop-mediated isothermal amplification (LAMP)-based detection. Here, we re-evaluated a published LAMP assay originally reported to detect 1 fg of P. agathidicida DNA. We found a reliable detection limit of 1000 fg. At 100 fg, amplification was variable, and no detection occurred at 10 fg or below. Although technical differences may affect sensitivity across laboratories, we were unable to replicate the reported detection limit. Laboratories should therefore verify assay performance under their own conditions and be aware that the sensitivity may be lower than expected.
","acknowledgements":"","authors":[{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","writing_originalDraft"],"email":"jade.palmer@vuw.ac.nz","firstName":"Jade TT","lastName":"Palmer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-6779-7638"},{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","project","resources","supervision","writing_reviewEditing"],"email":"monica.gerth@vuw.ac.nz","firstName":"Monica L","lastName":"Gerth","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-7959-7852"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Jade Palmer gratefully acknowledges PhD scholarship support from Victoria University of Wellington, Tiakina Kauri, the New Zealand Plant Protection Society, and Te Roroa Iwi.
","image":{"url":"https://portal.micropublication.org/uploads/9548ad527616aa6cdafe942ebcacfab3.jpg"},"imageCaption":"Amplification plots showing raw fluorescence over a 50-minute incubation. For each master mix, an independent 10-fold serial dilution of P. agathidicida genomic DNA (100,000 fg to 1 fg) was tested in technical triplicate (n=3). (A) Optigene Isothermal Master Mix. (B) NEB WarmStart LAMP Master Mix. Coloured lines represent the dilution series; the black dashed line represents the no-template control (ntc).
","imageTitle":"Comparison of P. agathidicida LAMP assay sensitivity and reproducibility across two master mixes
","methods":"DNA Extraction and Quantification
Genomic DNA was extracted from P. agathidicida strain NZFS 3770 mycelial mats grown in potato dextrose broth (Difco). Mats were grown until they covered approximately 50% of the surface of a 90 mm Petri dish. Harvested mats were rinsed with sterile water, blotted dry, and ground to a fine powder in liquid nitrogen. Total genomic DNA was extracted using the DNeasy Plant Mini kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen). For each assay, a fresh 10-fold serial dilution series (100,000 fg to 1 fg) was prepared in sterile PCR-grade water.
Primer Preparation
The primer sequences used in this study were originally described by (Winkworth et al., 2020) for the molecular detection of P. agathidicida. The lyophilised primers (Macrogen, Korea) were resuspended in low-EDTA TE buffer (10 mM Tris-HCl, 0.1 mM EDTA) to a stock concentration of 100 µM and stored at -20 °C. Working concentrations are provided in Table 1.
LAMP Assay Conditions and Data Analysis
Two reagent master mixes were evaluated: the original Optigene Isothermal Master Mix and the WarmStart Fluorescent LAMP Kit (with UDG; NEB). Each LAMP master mix was evaluated in triplicate, including a no-template control (NTC) using sterile PCR-grade water in place of genomic DNA for every run. The originally reported Optigene Isothermal Master Mix was used in 20 µL reactions incubated at 63 °C for 50 min. The alternative master mix, WarmStart Fluorescent LAMP Kit, was used in 25 µL reactions incubated at 65 °C for 50 min. All reactions were performed on a QuantStudio 3 Real-Time PCR System (Applied Biosystems) with fluorescence readings acquired every minute. Data were plotted and analysed using GraphPad Prism (v 11.0.0).
","reagents":"Primers | ||
Name | Sequence (5′ - 3′) | Final Concentration |
PTAF3 | TTATTTGAACCAACCTCATGT | 0.2 μM |
PTAB3 | TGTTTTACCTTGGGGACAA | 0.2 μM |
PTAFIP | GCTGTAGATAATCCAACTTTAAATCGTTTTGGTGTATTAATACGACCCCTAC | 0.6 μM |
PTABIP | CCACCCCATAGCCAATCAACAATATTTTGGGGTGCAACTGTT | 0.6 μM |
PTALF | TTAGTTTACATTTTACTTTTCCTTTTG | 0.4 μM |
PTALB | CCTATTAAAGGTATTGCAGAAAATAA | 0.4 μM |
Kits and Reagents | ||
Name (Supplier) | Catalogue Number | |
DNeasy Plant Mini kit (Qiagen) | 69104 | |
Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) | Q32854 | |
WarmStart Fluorescent LAMP Kit with UDG (New England Biolabs) | E1708 | |
Isothermal Master Mix (Optigene) | ISO-DR001 | |
Culture |
| |
Name | Source | |
Phytophthora agathidicida NZFS 3770 | Scion* |
*Also deposited in the International Collection Of Microorganisms as ICMP 17027.
","patternDescription":"Phytophthora agathidicida is the causal agent of kauri dieback disease in New Zealand. Sensitive, reliable detection of this plant pathogen is vital for effective disease management. Traditional detection methods rely on baiting soil samples followed by morphological identification (Beever et al., 2010; Tiakina Kauri, 2023). In 2020, a hybrid baiting/loop-mediated isothermal amplification (LAMP) assay was developed that applies LAMP directly to bait material, offering a faster alternative to culturing and morphological assessment (Winkworth et al., 2020). However, while the original publication reported a sensitivity of 1 fg, the data (Winkworth et al., 2020), Figure 3) did not include results for concentrations below 2 pg (2000 fg).
We initially explored using the P. agathidicida LAMP primers as part of a colorimetric, field-friendly workflow that could couple with our oospore DNA extraction method (Palmer & Gerth, 2025; Palmer et al., 2025). When the colorimetric assay failed to meet the expected performance, we undertook a replication study to assess the LAMP assay detection limit directly. The reported primers were tested against a dilution series of P. agathidicida genomic DNA using the original Optigene Isothermal Master Mix and an alternative New England Biolabs (NEB) WarmStart Master Mix.
No fluorescence was observed for either master mix at 1 fg or 10 fg. At 100 fg, the assay exhibited varible amplification; while all replicates produced a signal with the Optigene mix, they showed high variability in take-off time and morphology, with some curves remaining shallow-sloped (Figure 1A). Furthermore, one of the three Optigene no-template control (ntc) replicates exhibited both elevated initial background fluorescence and a non-specific increase starting at approximately 35 minutes. With the NEB mix, only one of three 100 fg replicates amplified; the ntc was more consistent, remaining at baseline for all three replicates (Figure 1B). Both master mixes yielded robust, uniform sigmoidal curves at 1000 fg, establishing this as the reliable limit of detection.
To ensure a direct replication of the original method, we maintained the reported F3/B3 and FIP/BIP concentrations. However, the published protocol omitted the concentrations for the Loop F/Loop B primers. In the absence of this detail, we used the manufacturer-recommended 0.4 mM final concentration (New England Biolabs, nd). While further optimisation of loop primer concentrations might improve performance, such iterative assay development was outside the scope of this replication study.
In conclusion, despite the previously reported sensitivity of 1 fg, this study found the LAMP assay’s reliable detection limit to be 1000 fg of P. agathidicida genomic DNA under both conditions tested. Although the assay received approval for use in kauri dieback surveillance (Tiakina Kauri, 2023), no replication study or accessible validation data have been publicly reported that would allow for direct technical comparison with our study. However, another laboratory has separately noted that the assay exhibited lower sensitivity than originally reported (Tomscha, 2026). While technical differences may affect sensitivity across laboratories, ultimately, we were unable to replicate the reported detection limit with the available methodological information. Laboratories should therefore verify assay performance under their own conditions and be aware that the sensitivity may be lower than expected. Together, these findings highlight the value of independent inter-laboratory validation to ensure methods are detailed enough for replication and that results are robust enough for reproducibility.
","references":[{"reference":"Beever, R. E., Bellgard, S. E., Dick, M. A., Horner, I. J., & Ramsfield, T. D. (2010). Detection of Phytophthora taxon Agathis (PTA). Landcare Research Report prepared for the Ministry for Agriculture & Forestry, Biosecurity New Zealand (on behalf of Kauri Dieback Joint Agency). https://www.kauriprotection.co.nz/assets/Research-reports/Surveillance-Detection-Diagnostics-and-Pathways/PA-Response-Research-Projects-Detection-of-Phytophthora-taxon-Agathis.pdf
","pubmedId":"","doi":""},{"reference":"New England Biolabs. WarmStart Multi-Purpose LAMP/RT-LAMP 2X Master Mix with UDG protocol. https://www.neb.com/en-nz/protocols/warmstart-multi-purpose-lamp-rt-lamp-2x-master-mix-with-udg-protocol-neb-m1078
","pubmedId":"","doi":""},{"reference":"Palmer JTT, Gerth ML. 2024. A Method for the Separation of Phytophthora Oospores from Soil for DNA-Based Detection. Methods in Molecular Biology, Phytophthora : 139-149.
","pubmedId":"","doi":"10.1007/978-1-0716-4330-3_10"},{"reference":"Palmer JTT, Vink JNA, Castro LM, Craig OJS, Davison EE, Gerth ML. 2025. Improved isolation and PCR detection of\n Phytophthora agathidicida\n oospores from soils. Microbiology Spectrum 13: 10.1128/spectrum.00135-25.
","pubmedId":"","doi":"10.1128/spectrum.00135-25"},{"reference":"Tiakina Kauri. (2023). Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/MPI-Approved-Test-Soil-bioassay-baiting-protocol-FINAL-June-2023.pdf
","pubmedId":"","doi":""},{"reference":"Tomscha, S. (2026). Approval of qPCR - A TaqMan real-time PCR (Than et al. 2013) for use in P. agathidicida surveillance and diagnostics. Tiakina Kauri, Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/Approval-of-qPCR.pdf
","pubmedId":"","doi":""},{"reference":"Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. 2020. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLOS ONE 15: e0224007.
","pubmedId":"","doi":"10.1371/journal.pone.0224007"}],"title":"Replication of a Phytophthora agathidicida LAMP assay is unsuccessful in achieving reported detection limits
","reviews":[],"curatorReviews":[]},{"id":"66123371-e6b1-4720-b38c-d3332ac0a9aa","decision":"revise","abstract":"Surveillance of Phytophthora agathidicida, the causal agent of kauri dieback, has relied on soil baiting and loop-mediated isothermal amplification (LAMP)-based detection. Here, we re-evaluated a published LAMP assay originally reported to detect 1 fg of P. agathidicida DNA. We found a reliable detection limit of 1000 fg. At 100 fg, amplification was variable, and no detection occurred at 10 fg or below. Although technical differences may affect sensitivity across laboratories, we were unable to replicate the reported detection limit. Laboratories should therefore verify assay performance under their own conditions and be aware that the sensitivity may be lower than expected.
","acknowledgements":"","authors":[{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","writing_originalDraft"],"email":"jade.palmer@vuw.ac.nz","firstName":"Jade TT","lastName":"Palmer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-6779-7638"},{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","project","resources","supervision","writing_reviewEditing"],"email":"monica.gerth@vuw.ac.nz","firstName":"Monica L","lastName":"Gerth","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-7959-7852"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Jade Palmer gratefully acknowledges PhD scholarship support from Victoria University of Wellington, Tiakina Kauri, the New Zealand Plant Protection Society, and Te Roroa Iwi.
","image":{"url":"https://portal.micropublication.org/uploads/9548ad527616aa6cdafe942ebcacfab3.jpg"},"imageCaption":"Amplification plots showing raw fluorescence over a 50-minute incubation. For each master mix, an independent 10-fold serial dilution of P. agathidicida genomic DNA (100,000 fg to 1 fg) was tested in technical triplicate (n=3). (A) Optigene Isothermal Master Mix. (B) NEB WarmStart LAMP Master Mix. Coloured lines represent the dilution series; the black dashed line represents the no-template control (ntc).
","imageTitle":"Comparison of P. agathidicida LAMP assay sensitivity and reproducibility across two master mixes
","methods":"DNA Extraction and Quantification
Genomic DNA was extracted from P. agathidicida strain NZFS 3770 mycelial mats grown in potato dextrose broth (Difco). Mats were grown until they covered approximately 50% of the surface of a 90 mm Petri dish. Harvested mats were rinsed with sterile water, blotted dry, and ground to a fine powder in liquid nitrogen. Total genomic DNA was extracted using the DNeasy Plant Mini kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen). For each assay, a fresh 10-fold serial dilution series (100,000 fg to 1 fg) was prepared in sterile PCR-grade water.
Primer Preparation
The primer sequences used in this study were originally described by (Winkworth et al., 2020) for the molecular detection of P. agathidicida. The lyophilised primers (Macrogen, Korea) were resuspended in low-EDTA TE buffer (10 mM Tris-HCl, 0.1 mM EDTA) to a stock concentration of 100 µM and stored at -20 °C. Working concentrations are provided in Table 1.
LAMP Assay Conditions and Data Analysis
Two reagent master mixes were evaluated: the original Optigene Isothermal Master Mix and the WarmStart Fluorescent LAMP Kit (with UDG; NEB). Each LAMP master mix was evaluated in triplicate, including a no-template control (NTC) using sterile PCR-grade water in place of genomic DNA for every run. The originally reported Optigene Isothermal Master Mix was used in 20 µL reactions incubated at 63 °C for 50 min. The alternative master mix, WarmStart Fluorescent LAMP Kit, was used in 25 µL reactions incubated at 65 °C for 50 min. All reactions were performed on a QuantStudio 3 Real-Time PCR System (Applied Biosystems) with fluorescence readings acquired every minute. Data were plotted and analysed using GraphPad Prism (v 11.0.0).
","reagents":"Primers | ||
Name | Sequence (5′ - 3′) | Final Concentration |
PTAF3 | TTATTTGAACCAACCTCATGT | 0.2 μM |
PTAB3 | TGTTTTACCTTGGGGACAA | 0.2 μM |
PTAFIP | GCTGTAGATAATCCAACTTTAAATCGTTTTGGTGTATTAATACGACCCCTAC | 0.6 μM |
PTABIP | CCACCCCATAGCCAATCAACAATATTTTGGGGTGCAACTGTT | 0.6 μM |
PTALF | TTAGTTTACATTTTACTTTTCCTTTTG | 0.4 μM |
PTALB | CCTATTAAAGGTATTGCAGAAAATAA | 0.4 μM |
Kits and Reagents | ||
Name (Supplier) | Catalogue Number | |
DNeasy Plant Mini kit (Qiagen) | 69104 | |
Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) | Q32854 | |
WarmStart Fluorescent LAMP Kit with UDG (New England Biolabs) | E1708 | |
Isothermal Master Mix (Optigene) | ISO-DR001 | |
Culture |
| |
Name | Source | |
Phytophthora agathidicida NZFS 3770 | Scion* |
*Also deposited in the International Collection Of Microorganisms as ICMP 17027.
","patternDescription":"Phytophthora agathidicida is the causal agent of kauri dieback disease in New Zealand. Sensitive, reliable detection of this plant pathogen is vital for effective disease management. Traditional detection methods rely on baiting soil samples followed by morphological identification (Beever et al., 2010; Tiakina Kauri, 2023). In 2020, a hybrid baiting/loop-mediated isothermal amplification (LAMP) assay was developed that applies LAMP directly to bait material, offering a faster alternative to culturing and morphological assessment (Winkworth et al., 2020). However, while the original publication reported a sensitivity of 1 fg, the data (Winkworth et al., 2020), Figure 3) did not include results for concentrations below 2 pg (2000 fg).
We initially explored using the P. agathidicida LAMP primers as part of a colorimetric, field-friendly workflow that could couple with our oospore DNA extraction method (Palmer & Gerth, 2025; Palmer et al., 2025). When the colorimetric assay failed to meet the expected performance, we undertook a replication study to assess the LAMP assay detection limit directly. The reported primers were tested against a dilution series of P. agathidicida genomic DNA using the original Optigene Isothermal Master Mix and an alternative New England Biolabs (NEB) WarmStart Master Mix.
No fluorescence was observed for either master mix at 1 fg or 10 fg. At 100 fg, the assay exhibited varible amplification; while all replicates produced a signal with the Optigene mix, they showed high variability in take-off time and morphology, with some curves remaining shallow-sloped (Figure 1A). Furthermore, one of the three Optigene no-template control (ntc) replicates exhibited both elevated initial background fluorescence and a non-specific increase starting at approximately 35 minutes. With the NEB mix, only one of three 100 fg replicates amplified; the ntc was more consistent, remaining at baseline for all three replicates (Figure 1B). Both master mixes yielded robust, uniform sigmoidal curves at 1000 fg, establishing this as the reliable limit of detection.
To ensure a direct replication of the original method, we maintained the reported F3/B3 and FIP/BIP concentrations. However, the published protocol omitted the concentrations for the Loop F/Loop B primers. In the absence of this detail, we used the manufacturer-recommended 0.4 μM final concentration (New England Biolabs, nd). While further optimisation of loop primer concentrations might improve performance, such iterative assay development was outside the scope of this replication study.
In conclusion, despite the previously reported sensitivity of 1 fg, this study found the LAMP assay’s reliable detection limit to be 1000 fg of P. agathidicida genomic DNA under both conditions tested. Although the assay received approval for use in kauri dieback surveillance (Tiakina Kauri, 2023), no replication study or accessible validation data have been publicly reported that would allow for direct technical comparison with our study. However, another laboratory has separately noted that the assay exhibited lower sensitivity than originally reported (Tomscha, 2026). While technical differences may affect sensitivity across laboratories, ultimately, we were unable to replicate the reported detection limit with the available methodological information. Laboratories should therefore verify assay performance under their own conditions and be aware that the sensitivity may be lower than expected. Together, these findings highlight the value of independent inter-laboratory validation to ensure methods are detailed enough for replication and that results are robust enough for reproducibility.
","references":[{"reference":"Beever, R. E., Bellgard, S. E., Dick, M. A., Horner, I. J., & Ramsfield, T. D. (2010). Detection of Phytophthora taxon Agathis (PTA). Landcare Research Report prepared for the Ministry for Agriculture & Forestry, Biosecurity New Zealand (on behalf of Kauri Dieback Joint Agency). https://www.kauriprotection.co.nz/assets/Research-reports/Surveillance-Detection-Diagnostics-and-Pathways/PA-Response-Research-Projects-Detection-of-Phytophthora-taxon-Agathis.pdf
","pubmedId":"","doi":""},{"reference":"New England Biolabs. WarmStart Multi-Purpose LAMP/RT-LAMP 2X Master Mix with UDG protocol. https://www.neb.com/en-nz/protocols/warmstart-multi-purpose-lamp-rt-lamp-2x-master-mix-with-udg-protocol-neb-m1078
","pubmedId":"","doi":""},{"reference":"Palmer JTT, Gerth ML. 2024. A Method for the Separation of Phytophthora Oospores from Soil for DNA-Based Detection. Methods in Molecular Biology, Phytophthora : 139-149.
","pubmedId":"","doi":"10.1007/978-1-0716-4330-3_10"},{"reference":"Palmer JTT, Vink JNA, Castro LM, Craig OJS, Davison EE, Gerth ML. 2025. Improved isolation and PCR detection of\n Phytophthora agathidicida\n oospores from soils. Microbiology Spectrum 13: 10.1128/spectrum.00135-25.
","pubmedId":"","doi":"10.1128/spectrum.00135-25"},{"reference":"Tiakina Kauri. (2023). Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/MPI-Approved-Test-Soil-bioassay-baiting-protocol-FINAL-June-2023.pdf
","pubmedId":"","doi":""},{"reference":"Tomscha, S. (2026). Approval of qPCR - A TaqMan real-time PCR (Than et al. 2013) for use in P. agathidicida surveillance and diagnostics. Tiakina Kauri, Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/Approval-of-qPCR.pdf
","pubmedId":"","doi":""},{"reference":"Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. 2020. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLOS ONE 15: e0224007.
","pubmedId":"","doi":"10.1371/journal.pone.0224007"}],"title":"Replication of a Phytophthora agathidicida LAMP assay is unsuccessful in achieving reported detection limits
","reviews":[{"reviewer":{"displayName":"Richard Winkworth"},"openAcknowledgement":true,"status":{"submitted":true}},{"reviewer":{"displayName":"Joel Vanneste"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"bc3082b2-98d8-4ad4-bf13-7947adbbedca","decision":"accept","abstract":"Surveillance of Phytophthora agathidicida, the causal agent of kauri dieback, has used on soil baiting followed by loop-mediated isothermal amplification (LAMP)-based detection. This approved assay was reported to detect 1 fg of DNA using OptiGene Isothermal Mastermix on a BioRanger instrument. We evaluated its analytical robustness using the same master mix on an alternative platform (QuantStudio 3), and separately tested an alternative NEB master mix. Both assays yielded a reliable detection limit of 1,000 fg, with variable detection at 100 fg and none below. Diagnostic laboratories should verify assay performance under their operational conditions prior to implementation.
","acknowledgements":"","authors":[{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","writing_originalDraft"],"email":"jade.palmer@vuw.ac.nz","firstName":"Jade TT","lastName":"Palmer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-6779-7638"},{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","project","resources","supervision","writing_reviewEditing"],"email":"monica.gerth@vuw.ac.nz","firstName":"Monica L","lastName":"Gerth","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-7959-7852"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Jade Palmer gratefully acknowledges PhD scholarship support from Victoria University of Wellington, Tiakina Kauri, the New Zealand Plant Protection Society, and Te Roroa Iwi.
","image":{"url":"https://portal.micropublication.org/uploads/9548ad527616aa6cdafe942ebcacfab3.jpg"},"imageCaption":"Amplification plots showing raw fluorescence over a 50-minute incubation. For each master mix, an independent 10-fold serial dilution of P. agathidicida genomic DNA (100,000 fg to 1 fg) was tested in technical triplicate (n=3). (A) Optigene Isothermal Master Mix. (B) NEB WarmStart LAMP Master Mix. Coloured lines represent the dilution series; the black dashed line represents the no-template control (ntc).
","imageTitle":"Comparison of P. agathidicida LAMP assay sensitivity and reproducibility across two master mixes
","methods":"DNA Extraction and Quantification
Genomic DNA was extracted from P. agathidicida strain NZFS 3770 mycelial mats grown in potato dextrose broth (Difco). Mats were grown until they covered approximately 50% of the surface of a 90 mm Petri dish. Harvested mats were rinsed with sterile water, blotted dry, and ground to a fine powder in liquid nitrogen. Total genomic DNA was extracted using the DNeasy Plant Mini kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen). For each assay, a fresh 10-fold serial dilution series (100,000 fg to 1 fg) was prepared in sterile PCR-grade water.
Primer Preparation
The primer sequences used in this study were originally described by (Winkworth et al., 2020) for the molecular detection of P. agathidicida. The lyophilised primers (Macrogen, Korea) were resuspended in low-EDTA TE buffer (10 mM Tris-HCl, 0.1 mM EDTA) to a stock concentration of 100 µM and stored at -20 °C. Working concentrations are provided in the Reagents section below.
LAMP Assay Conditions and Data Analysis
Two reagent master mixes were evaluated: the original Optigene Isothermal Master Mix and the WarmStart Fluorescent LAMP Kit (with UDG; NEB). Each LAMP master mix was evaluated in triplicate, including a no-template control (NTC) using sterile PCR-grade water in place of genomic DNA for every run. The originally reported OptiGene Isothermal Master Mix was used in 20 µL reactions incubated at 63 °C for 50 min. The alternative master mix, WarmStart Fluorescent LAMP Kit, was used in 25 µL reactions incubated at 65 °C for 50 min. All reactions were performed on a QuantStudio 3 Real-Time PCR System (Applied Biosystems) with fluorescence readings acquired every minute. Data were plotted and analysed using GraphPad Prism (v 11.0.0).
","reagents":"Primers | ||
Name | Sequence (5′ - 3′) | Final Concentration |
PTAF3 | TTATTTGAACCAACCTCATGT | 0.2 μM |
PTAB3 | TGTTTTACCTTGGGGACAA | 0.2 μM |
PTAFIP | GCTGTAGATAATCCAACTTTAAATCGTTTTGGTGTATTAATACGACCCCTAC | 0.6 μM |
PTABIP | CCACCCCATAGCCAATCAACAATATTTTGGGGTGCAACTGTT | 0.6 μM |
PTALF | TTAGTTTACATTTTACTTTTCCTTTTG | 0.4 μM |
PTALB | CCTATTAAAGGTATTGCAGAAAATAA | 0.4 μM |
Kits and Reagents | ||
Name (Supplier) | Catalogue Number | |
DNeasy Plant Mini kit (Qiagen) | 69104 | |
Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) | Q32854 | |
WarmStart Fluorescent LAMP Kit with UDG (New England Biolabs) | E1708 | |
Isothermal Master Mix (OptiGene) | ISO-DR001 | |
Culture |
| |
Name | Source | |
Phytophthora agathidicida NZFS 3770 | Scion* |
*Also deposited in the International Collection Of Microorganisms as ICMP 17027.
","patternDescription":"Phytophthora agathidicida is the causal agent of kauri dieback disease in New Zealand. Sensitive and reliable detection of this plant pathogen is vital for effective disease management. Traditional detection methods rely on soil baiting followed by morphological identification (Beever et al., 2010; Tiakina Kauri, 2023). In 2020, a hybrid baiting/loop-mediated isothermal amplification (LAMP) assay was developed that applies LAMP directly to bait material, offering a faster alternative to culturing (Winkworth et al., 2020). The original assay was optimised and validated using OptiGene Isothermal Master Mix on a dedicated LAMP instrument (BioRanger, Diagenetix Inc.), reporting a limit of detection of 1 fg of total P. agathidicida DNA.
We initially explored using the P. agathidicida LAMP primers as part of a colorimetric, field-friendly workflow designed to couple with our oospore DNA extraction method (Palmer & Gerth, 2025; Palmer et al., 2025). Initial testing yielded poor sensitivity, which was not unexpected given that colorimetric readouts can exhibit reduced sensitivity relative to fluorometric detection (Aglietti et al., 2024). To investigate further, we re-examined the baseline assay performance in the literature. While an analytical sensitivity of 1 fg was reported in the text, the published amplification plots presented data down to 2 pg (2,000 fg; Winkworth et al., 2020). To clarify performance at these lower concentrations, we undertook a study to directly assess the assay's limit of detection under real-time fluorescent conditions.
We attempted to replicate the reported conditions as closely as possible, using the same master mix (OptiGene Isothermal Master Mix), reported primer concentrations (F3/B3 and FIP/BIP), and incubation temperature (63°C) as the original study (Winkworth et al., 2020). The published protocol did not report Loop F/Loop B primer concentrations, so we used the OptiGene manufacturer-recommended 0.4 µM final concentration (OptiGene, nd). We did not have access to a BioRanger instrument, as Diagenetix, Inc. ceased operations in 2023 (PitchBook, 2026). Instead, we used a QuantStudio 3 Real-Time PCR System (Applied Biosystems). While there is precedent in the literature for using real-time PCR platforms for LAMP fluorescence detection (García-Bernalt Diego et al., 2022; Stehlíková et al., 2020), instrument hardware was a primary variable differing from the original protocol. In a second experimental condition, we trialled NEB WarmStart Fluorescent LAMP Master Mix at its recommended incubation temperature (65°C), maintaining the 0.4 µM Loop F/Loop B primer concentration in line with standard NEB guidelines (New England Biolabs, nd). Reaction parameters (including primer ratios and incubation temperatures) were not independently re-optimised for either master mix on the QuantStudio platform; assay re-optimisation could plausibly improve performance, but was outside the scope of the present study.
No fluorescence was observed for either master mix at 1 fg or 10 fg. At 100 fg, amplification was variable: all OptiGene replicates produced a signal, but with high variability in take-off time and curve morphology, and one of three OptiGene no-template control (NTC) replicates showed both elevated initial background fluorescence and a non-specific fluorescence increase beginning at approximately 35 minutes (Figure 1A). This anomaly was specific to the OptiGene mix and was not observed with the NEB mix on the same QuantStudio 3 platform; we therefore cannot exclude a chemistry-specific artefact as a contributor to the variability seen at 100 fg with the OptiGene mix, which complicates interpretation of these particular data. With the NEB mix, only one of three 100 fg replicates amplified, while NTCs remained at baseline in all three replicates (Figure 1B). Both master mixes yielded robust, uniform sigmoidal curves at 1,000 fg.
Overall, under the experimental conditions tested here, we established a reliable detection limit of 1,000 fg for the P. agathidicida LAMP assay. We acknowledge that our study does not represent a direct, same-methods replication, which would require the original BioRanger instrument and exact original protocol. Instead, it evaluates assay reproducibility and robustness (Schloss, 2018), testing whether reported performance holds across alternative platforms and/or reagents. Although this LAMP assay remains officially approved for kauri dieback surveillance (Tiakina Kauri, 2023), the commercial unavailability of the BioRanger means operationalising it today inevitably requires platform adaptation. To date, no public inter-laboratory validation data exist to support such platform substitutions — a notable gap given that formal diagnostic validation frameworks treat multi-laboratory, multi-platform transferability as an essential tier for decentralised deployment (Tier 3; Cardwell et al., 2018; Groth-Helms et al., 2023). One report (Tomscha, 2026) notes an in-house comparison by the Ministry for Primary Industries’ Plant Health and Environment Laboratory that found a TaqMan qPCR assay (Than et al., 2013) to be more sensitive than the LAMP assay, without disclosing the obtained detection limits or methods used.
While these findings should not be construed as a failure of the original protocol under its specific conditions, they demonstrate that the assay's sensitivity is potentially not robust to platform or reagent substitution. Laboratories intending to deploy this approved workflow on alternative instruments should independently verify and re-optimise assay performance prior to relying on it for biosecurity decision-making.
","references":[{"reference":"Aglietti C, Benigno A, Cacciola SO, Moricca S. 2024. LAMP Reaction in Plant Disease Surveillance: Applications, Challenges, and Future Perspectives. Life 14: 1549.
","pubmedId":"","doi":"10.3390/life14121549"},{"reference":"Beever, R. E., Bellgard, S. E., Dick, M. A., Horner, I. J., & Ramsfield, T. D. (2010). Detection of Phytophthora taxon Agathis (PTA). Landcare Research Report prepared for the Ministry for Agriculture & Forestry, Biosecurity New Zealand (on behalf of Kauri Dieback Joint Agency). https://www.kauriprotection.co.nz/assets/Research-reports/Surveillance-Detection-Diagnostics-and-Pathways/PA-Response-Research-Projects-Detection-of-Phytophthora-taxon-Agathis.pdf
","pubmedId":"","doi":""},{"reference":"Cardwell K, Dennis G, Flannery AR, Fletcher J, Luster D, Nakhla M, et al., Levy. 2018. Principles of Diagnostic Assay Validation for Plant Pathogens: A Basic Review of Concepts. Plant Health Progress 19: 272-278.
","pubmedId":"","doi":"10.1094/PHP-06-18-0036-RV"},{"reference":"García-Bernalt Diego J, Fernández-Soto P, Márquez-Sánchez S, Santos Santos D, Febrer-Sendra Ba, Crego-Vicente B, et al., Muro. 2022. SMART-LAMP: A Smartphone-Operated Handheld Device for Real-Time Colorimetric Point-of-Care Diagnosis of Infectious Diseases via Loop-Mediated Isothermal Amplification. Biosensors 12: 424.
","pubmedId":"","doi":"10.3390/bios12060424"},{"reference":"Groth-Helms D, Rivera Yn, Martin FN, Arif M, Sharma P, Castlebury LA. 2023. Terminology and Guidelines for Diagnostic Assay Development and Validation: Best Practices for Molecular Tests. PhytoFrontiers 3: 23-35.
","pubmedId":"","doi":"10.1094/PHYTOFR-05-22-0059-FI"},{"reference":"New England Biolabs. WarmStart Multi-Purpose LAMP/RT-LAMP 2X Master Mix with UDG protocol. https://www.neb.com/en-nz/protocols/warmstart-multi-purpose-lamp-rt-lamp-2x-master-mix-with-udg-protocol-neb-m1078
","pubmedId":"","doi":""},{"reference":"OptiGene. LAMP User Guide – Assay Design & Primers. https://www.optigene.co.uk/wp-content/uploads/2012/06/OptiGene-LAMP-User-Guide-Assay-Design-Primers-1.pdf
","pubmedId":"","doi":""},{"reference":"Palmer JTT, Gerth ML. 2025. A Method for the Separation of Phytophthora Oospores from Soil for DNA-Based Detection. Methods in Molecular Biology, Phytophthora : 139-149.
","pubmedId":"","doi":"10.1007/978-1-0716-4330-3_10"},{"reference":"Palmer JTT, Vink JNA, Castro LM, Craig OJS, Davison EE, Gerth ML. 2025. Improved isolation and PCR detection of\n Phytophthora agathidicida\n oospores from soils. Microbiology Spectrum 13: 10.1128/spectrum.00135-25.
","pubmedId":"","doi":"10.1128/spectrum.00135-25"},{"reference":"PitchBook. (2026). Diagenetix company profile. https://pitchbook.com/profiles/company/112919-32
","pubmedId":"","doi":""},{"reference":"Schloss PD. 2018. Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research. mBio 9(3): 10.1128/mBio.00525-18.
","pubmedId":"29871915","doi":""},{"reference":"Stehlíková D, Beran P, Cohen SP, Čurn V. 2020. Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 8(9): 10.3390/microorganisms8091301.
","pubmedId":"32858943","doi":""},{"reference":"Tiakina Kauri. (2023). Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/MPI-Approved-Test-Soil-bioassay-baiting-protocol-FINAL-June-2023.pdf
","pubmedId":"","doi":""},{"reference":"Tomscha, S. (2026). Approval of qPCR - A TaqMan real-time PCR (Than et al. 2013) for use in P. agathidicida surveillance and diagnostics. Tiakina Kauri, Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/Approval-of-qPCR.pdf
","pubmedId":"","doi":""},{"reference":"Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. 2020. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLOS ONE 15: e0224007.
","pubmedId":"","doi":"10.1371/journal.pone.0224007"}],"title":"The limit of detection of a Phytophthora agathidicida LAMP assay is higher under alternative laboratory conditions
","reviews":[{"reviewer":{"displayName":"Richard Winkworth"},"openAcknowledgement":true,"status":{"submitted":true}},{"reviewer":{"displayName":"Jie Feng"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"01db959c-7002-475f-a8ee-a2138780090c","decision":"accept","abstract":"Surveillance of Phytophthora agathidicida, the causal agent of kauri dieback, has included soil baiting followed by loop-mediated isothermal amplification (LAMP)-based detection. This approved assay was reported to detect 1 fg of DNA using OptiGene Isothermal Master Mix on a BioRanger instrument. We evaluated its analytical robustness using the same master mix on an alternative platform (QuantStudio 3), and separately tested an alternative NEB master mix. Both assays yielded a reliable detection limit of 1,000 fg, with variable detection at 100 fg and none below. Diagnostic laboratories should verify assay performance under their operational conditions prior to implementation.
","acknowledgements":"","authors":[{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","writing_originalDraft"],"email":"jade.palmer@vuw.ac.nz","firstName":"Jade TT","lastName":"Palmer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-6779-7638"},{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","project","resources","supervision","writing_reviewEditing"],"email":"monica.gerth@vuw.ac.nz","firstName":"Monica L","lastName":"Gerth","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-7959-7852"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Jade Palmer gratefully acknowledges PhD scholarship support from Victoria University of Wellington, Tiakina Kauri, the New Zealand Plant Protection Society, and Te Roroa Iwi.
","image":{"url":"https://portal.micropublication.org/uploads/9548ad527616aa6cdafe942ebcacfab3.jpg"},"imageCaption":"Amplification plots showing raw fluorescence over a 50-minute incubation. For each master mix, an independent 10-fold serial dilution of P. agathidicida genomic DNA (100,000 fg to 1 fg) was tested in technical triplicate (n=3). (A) OptiGene Isothermal Master Mix. (B) NEB WarmStart LAMP Master Mix. Coloured lines represent the dilution series; the black dashed line represents the no-template control (ntc).
","imageTitle":"Comparison of P. agathidicida LAMP assay sensitivity and reproducibility across two master mixes
","methods":"DNA Extraction and Quantification
Genomic DNA was extracted from P. agathidicida strain NZFS 3770 mycelial mats grown in potato dextrose broth (Difco). Mats were grown until they covered approximately 50% of the surface of a 90 mm Petri dish. Harvested mats were rinsed with sterile water, blotted dry, and ground to a fine powder in liquid nitrogen. Total genomic DNA was extracted using the DNeasy Plant Mini kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen). For each assay, a fresh 10-fold serial dilution series (100,000 fg to 1 fg) was prepared in sterile PCR-grade water.
Primer Preparation
The primer sequences used in this study were originally described by (Winkworth et al., 2020) for the molecular detection of P. agathidicida. The lyophilised primers (Macrogen, Korea) were resuspended in low-EDTA TE buffer (10 mM Tris-HCl, 0.1 mM EDTA) to a stock concentration of 100 µM and stored at -20 °C. Working concentrations are provided in the Reagents section below.
LAMP Assay Conditions and Data Analysis
Two reagent master mixes were evaluated: the original OptiGene Isothermal Master Mix and the WarmStart Fluorescent LAMP Kit (with UDG; NEB). Each LAMP master mix was evaluated in triplicate, including a no-template control (NTC) using sterile PCR-grade water in place of genomic DNA for every run. The originally reported OptiGene Isothermal Master Mix was used in 20 µL reactions incubated at 63 °C for 50 min. The alternative master mix, WarmStart Fluorescent LAMP Kit, was used in 25 µL reactions incubated at 65 °C for 50 min. All reactions were performed on a QuantStudio 3 Real-Time PCR System (Applied Biosystems) with fluorescence readings acquired every minute. Data were plotted and analysed using GraphPad Prism (v 11.0.0).
","reagents":"Primers | ||
Name | Sequence (5′ - 3′) | Final Concentration |
PTAF3 | TTATTTGAACCAACCTCATGT | 0.2 μM |
PTAB3 | TGTTTTACCTTGGGGACAA | 0.2 μM |
PTAFIP | GCTGTAGATAATCCAACTTTAAATCGTTTTGGTGTATTAATACGACCCCTAC | 0.6 μM |
PTABIP | CCACCCCATAGCCAATCAACAATATTTTGGGGTGCAACTGTT | 0.6 μM |
PTALF | TTAGTTTACATTTTACTTTTCCTTTTG | 0.4 μM |
PTALB | CCTATTAAAGGTATTGCAGAAAATAA | 0.4 μM |
Kits and Reagents | ||
Name (Supplier) | Catalogue Number | |
DNeasy Plant Mini kit (Qiagen) | 69104 | |
Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) | Q32854 | |
WarmStart Fluorescent LAMP Kit with UDG (New England Biolabs) | E1708 | |
Isothermal Master Mix (OptiGene) | ISO-DR001 | |
Culture |
| |
Name | Source | |
Phytophthora agathidicida NZFS 3770 | Scion* |
*Also deposited in the International Collection of Microorganisms as ICMP 17027.
","patternDescription":"Phytophthora agathidicida is the causal agent of kauri dieback disease in New Zealand. Sensitive and reliable detection of this plant pathogen is vital for effective disease management. Traditional detection methods rely on soil baiting followed by morphological identification (Beever et al., 2010; Tiakina Kauri, 2023). In 2020, a hybrid baiting/loop-mediated isothermal amplification (LAMP) assay was reported that applies LAMP directly to bait material, offering a faster alternative to culturing (Winkworth et al., 2020). The original assay was optimised and validated using OptiGene Isothermal Master Mix on a dedicated LAMP instrument (BioRanger, Diagenetix Inc.), reporting a limit of detection of 1 fg of total P. agathidicida DNA.
We initially explored using the P. agathidicida LAMP primers as part of a colorimetric, field-friendly workflow designed to couple with our oospore DNA extraction method (Palmer & Gerth, 2025; Palmer et al., 2025). Initial testing yielded poor sensitivity, which was not unexpected given that colorimetric readouts can exhibit reduced sensitivity relative to fluorometric detection (Aglietti et al., 2024). To investigate further, we re-examined the baseline assay performance in the literature. While an analytical sensitivity of 1 fg was reported in the text, the published amplification plots presented data down to 2 pg (2,000 fg; Winkworth et al., 2020). To clarify performance at lower concentrations, we undertook a study to directly assess the assay's limit of detection under real-time fluorescent conditions.
We attempted to replicate the reported conditions as closely as possible, using the same master mix (OptiGene Isothermal Master Mix), reported primer concentrations (F3/B3 and FIP/BIP), and incubation temperature (63 °C) as the original study (Winkworth et al., 2020). The published protocol did not report Loop F/Loop B primer concentrations, so we used the OptiGene manufacturer-recommended 0.4 µM final concentration (OptiGene, n.d.). We did not have access to a BioRanger instrument, as Diagenetix, Inc. ceased operations in 2023 (PitchBook, 2026). Instead, we used a QuantStudio 3 Real-Time PCR System (Applied Biosystems). While there is precedent in the literature for using real-time PCR platforms for LAMP fluorescence detection (García-Bernalt Diego et al., 2022; Stehlíková et al., 2020), instrument hardware was a primary variable differing from the original protocol. In a second experimental condition, we trialled NEB WarmStart Fluorescent LAMP Master Mix at its recommended incubation temperature (65 °C), maintaining the 0.4 µM Loop F/Loop B primer concentration in line with standard NEB guidelines (New England Biolabs, n.d.). Reaction parameters (including primer ratios and incubation temperatures) were not independently re-optimised for either master mix on the QuantStudio platform; assay re-optimisation could plausibly improve performance, but was outside the scope of the present study.
No fluorescence was observed for either master mix at 1 fg or 10 fg. At 100 fg, amplification was variable: all OptiGene replicates produced a signal, but with high variability in take-off time and curve morphology, and one of three OptiGene no-template control (NTC) replicates showed both elevated initial background fluorescence and a non-specific fluorescence increase beginning at approximately 35 minutes (Figure 1A). This anomaly was specific to the OptiGene mix and was not observed with the NEB mix on the same QuantStudio 3 platform; we therefore cannot exclude a chemistry-specific artefact as a contributor to the variability seen at 100 fg with the OptiGene mix, which complicates interpretation of these particular data. With the NEB mix, only one of three 100 fg replicates amplified, while NTCs remained at baseline in all three replicates (Figure 1B). Both master mixes yielded robust, uniform sigmoidal curves at 1,000 fg.
Overall, under the experimental conditions tested here, we established a reliable detection limit of 1,000 fg for the P. agathidicida LAMP assay. We acknowledge that our study does not represent a direct, same-methods replication, which would require the original BioRanger instrument and exact original protocol. Instead, it evaluates assay reproducibility and robustness (Schloss, 2018), testing whether reported performance holds across alternative platforms and/or reagents. Although this LAMP assay remains officially approved for kauri dieback surveillance (Tiakina Kauri, 2023), the commercial unavailability of the BioRanger means operationalising it today inevitably requires platform adaptation. To date, no public inter-laboratory validation data exist to support such platform substitutions — a notable gap given that formal diagnostic validation frameworks treat multi-laboratory, multi-platform transferability as an essential tier for decentralised deployment (Tier 3; Cardwell et al., 2018; Groth-Helms et al., 2023). One report (Tomscha, 2026) notes an in-house comparison by the Ministry for Primary Industries’ Plant Health and Environment Laboratory that found a TaqMan qPCR assay (Than et al., 2013) to be more sensitive than the LAMP assay, without disclosing the obtained detection limits or methods used.
While these findings should not be construed as a failure of the original protocol under its specific conditions, they suggest that the assay's sensitivity is potentially not robust to platform or reagent substitution. Laboratories intending to deploy this approved workflow on alternative instruments should independently verify and re-optimise assay performance prior to relying on it for biosecurity decision-making.
","references":[{"reference":"Aglietti C, Benigno A, Cacciola SO, Moricca S. 2024. LAMP Reaction in Plant Disease Surveillance: Applications, Challenges, and Future Perspectives. Life 14: 1549.
","pubmedId":"","doi":"10.3390/life14121549"},{"reference":"Beever, RE, Bellgard, SE, Dick, MA, Horner, IJ, & Ramsfield, TD. 2010. Detection of Phytophthora taxon Agathis (PTA). Landcare Research Report prepared for the Ministry for Agriculture & Forestry, Biosecurity New Zealand (on behalf of Kauri Dieback Joint Agency). https://www.kauriprotection.co.nz/assets/Research-reports/Surveillance-Detection-Diagnostics-and-Pathways/PA-Response-Research-Projects-Detection-of-Phytophthora-taxon-Agathis.pdf
","pubmedId":"","doi":""},{"reference":"Cardwell K, Dennis G, Flannery AR, Fletcher J, Luster D, Nakhla M, et al., Levy. 2018. Principles of Diagnostic Assay Validation for Plant Pathogens: A Basic Review of Concepts. Plant Health Progress 19: 272-278.
","pubmedId":"","doi":"10.1094/PHP-06-18-0036-RV"},{"reference":"García-Bernalt Diego J, Fernández-Soto P, Márquez-Sánchez S, Santos Santos D, Febrer-Sendra Ba, Crego-Vicente B, et al., Muro. 2022. SMART-LAMP: A Smartphone-Operated Handheld Device for Real-Time Colorimetric Point-of-Care Diagnosis of Infectious Diseases via Loop-Mediated Isothermal Amplification. Biosensors 12: 424.
","pubmedId":"","doi":"10.3390/bios12060424"},{"reference":"Groth-Helms D, Rivera Y, Martin FN, Arif M, Sharma P, Castlebury LA. 2023. Terminology and Guidelines for Diagnostic Assay Development and Validation: Best Practices for Molecular Tests. PhytoFrontiers 3: 23-35.
","pubmedId":"","doi":"10.1094/PHYTOFR-05-22-0059-FI"},{"reference":"New England Biolabs. WarmStart Multi-Purpose LAMP/RT-LAMP 2X Master Mix with UDG protocol. https://www.neb.com/en-nz/protocols/warmstart-multi-purpose-lamp-rt-lamp-2x-master-mix-with-udg-protocol-neb-m1078
","pubmedId":"","doi":""},{"reference":"OptiGene. LAMP User Guide – Assay Design & Primers. https://www.optigene.co.uk/wp-content/uploads/2012/06/OptiGene-LAMP-User-Guide-Assay-Design-Primers-1.pdf
","pubmedId":"","doi":""},{"reference":"Palmer JTT, Gerth ML. 2025. A Method for the Separation of Phytophthora Oospores from Soil for DNA-Based Detection. Methods in Molecular Biology, Phytophthora. 2892:139-149.
","pubmedId":"","doi":"10.1007/978-1-0716-4330-3_10"},{"reference":"Palmer JTT, Vink JNA, Castro LM, Craig OJS, Davison EE, Gerth ML. 2025. Improved isolation and PCR detection of Phytophthora agathidicida oospores from soils. Microbiology Spectrum.
","pubmedId":"","doi":"10.1128/spectrum.00135-25"},{"reference":"PitchBook. 2026. Diagenetix company profile. https://pitchbook.com/profiles/company/112919-32
","pubmedId":"","doi":""},{"reference":"Schloss PD. 2018. Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research. mBio 9(3):e00525-18. PMID: 29871915
","pubmedId":"","doi":"10.1128/mBio.00525-18"},{"reference":"Stehlíková D, Beran P, Cohen SP, Čurn V. 2020. Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 8(9):
","pubmedId":"32858943","doi":"10.3390/microorganisms8091301"},{"reference":"Than DJ, Hughes KJD, Boonhan N, Tomlinson JA, Woodhall JW, Bellgard SE. 2013. A
Tiakina Kauri. 2023. Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/MPI-Approved-Test-Soil-bioassay-baiting-protocol-FINAL-June-2023.pdf
","pubmedId":"","doi":""},{"reference":"Tomscha, S. 2026. Approval of qPCR - A TaqMan real-time PCR (Than et al. 2013) for use in P. agathidicida surveillance and diagnostics. Tiakina Kauri, Ministry for Primary Industries. https://www.kauriprotection.co.nz/assets/content-blocks/downloads/Approval-of-qPCR.pdf
","pubmedId":"","doi":""},{"reference":"Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. 2020. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLOS ONE 15: e0224007.
","pubmedId":"","doi":"10.1371/journal.pone.0224007"}],"title":"The limit of detection of a Phytophthora agathidicida LAMP assay is higher under alternative laboratory conditions
","reviews":[],"curatorReviews":[]},{"id":"26e949d0-08f4-42e0-8f75-35490429f7af","decision":"edit","abstract":"Surveillance of Phytophthora agathidicida, the causal agent of kauri dieback, has included soil baiting followed by loop-mediated isothermal amplification (LAMP)-based detection. This approved assay was reported to detect 1 fg of DNA using OptiGene Isothermal Master Mix on a BioRanger instrument. We evaluated its analytical robustness using the same master mix on an alternative platform (QuantStudio 3), and separately tested an alternative NEB master mix. Both assays yielded a reliable detection limit of 1,000 fg, with variable detection at 100 fg and none below. Diagnostic laboratories should verify assay performance under their operational conditions prior to implementation.
","acknowledgements":"","authors":[{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","writing_originalDraft"],"email":"jade.palmer@vuw.ac.nz","firstName":"Jade TT","lastName":"Palmer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-6779-7638"},{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","project","resources","supervision","writing_reviewEditing"],"email":"monica.gerth@vuw.ac.nz","firstName":"Monica L","lastName":"Gerth","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-7959-7852"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Jade Palmer gratefully acknowledges PhD scholarship support from Victoria University of Wellington, Tiakina Kauri, the New Zealand Plant Protection Society, and Te Roroa Iwi.
","image":{"url":"https://portal.micropublication.org/uploads/9548ad527616aa6cdafe942ebcacfab3.jpg"},"imageCaption":"Amplification plots showing raw fluorescence over a 50-minute incubation. For each master mix, an independent 10-fold serial dilution of P. agathidicida genomic DNA (100,000 fg to 1 fg) was tested in technical triplicate (n=3). (A) OptiGene Isothermal Master Mix. (B) NEB WarmStart Fluorescent LAMP Master Mix. Coloured lines represent the dilution series; the black dashed line represents the no-template control (ntc).
","imageTitle":"Comparison of P. agathidicida LAMP assay sensitivity and reproducibility across two master mixes
","methods":"DNA Extraction and Quantification
Genomic DNA was extracted from P. agathidicida strain NZFS 3770 mycelial mats grown in potato dextrose broth (Difco). Mats were grown until they covered approximately 50% of the surface of a 90 mm Petri dish. Harvested mats were rinsed with sterile water, blotted dry, and ground to a fine powder in liquid nitrogen. Total genomic DNA was extracted using the DNeasy Plant Mini kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen). For each assay, a fresh 10-fold serial dilution series (100,000 fg to 1 fg) was prepared in sterile PCR-grade water.
Primer Preparation
The primer sequences used in this study were originally described by (Winkworth et al., 2020) for the molecular detection of P. agathidicida. The lyophilised primers (Macrogen, Korea) were resuspended in low-EDTA TE buffer (10 mM Tris-HCl, 0.1 mM EDTA) to a stock concentration of 100 µM and stored at -20 °C. Working concentrations are provided in the Reagents section below.
LAMP Assay Conditions and Data Analysis
Two reagent master mixes were evaluated: the original OptiGene Isothermal Master Mix and the WarmStart Fluorescent LAMP Kit (with UDG; NEB). Each LAMP master mix was evaluated in triplicate, including a no-template control (NTC) using sterile PCR-grade water in place of genomic DNA for every run. The originally reported OptiGene Isothermal Master Mix was used in 20 µL reactions incubated at 63 °C for 50 min. The alternative master mix, WarmStart Fluorescent LAMP Kit, was used in 25 µL reactions incubated at 65 °C for 50 min. All reactions were performed on a QuantStudio 3 Real-Time PCR System (Applied Biosystems) with fluorescence readings acquired every minute. Data were plotted and analysed using GraphPad Prism (v 11.0.0).
","reagents":"Primers | ||
Name | Sequence (5′ - 3′) | Final Concentration |
PTAF3 | TTATTTGAACCAACCTCATGT | 0.2 μM |
PTAB3 | TGTTTTACCTTGGGGACAA | 0.2 μM |
PTAFIP | GCTGTAGATAATCCAACTTTAAATCGTTTTGGTGTATTAATACGACCCCTAC | 0.6 μM |
PTABIP | CCACCCCATAGCCAATCAACAATATTTTGGGGTGCAACTGTT | 0.6 μM |
PTALF | TTAGTTTACATTTTACTTTTCCTTTTG | 0.4 μM |
PTALB | CCTATTAAAGGTATTGCAGAAAATAA | 0.4 μM |
Kits and Reagents | ||
Name (Supplier) | Catalogue Number | |
DNeasy Plant Mini kit (Qiagen) | 69104 | |
Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) | Q32854 | |
WarmStart Fluorescent LAMP Kit with UDG (New England Biolabs) | E1708 | |
Isothermal Master Mix (OptiGene) | ISO-DR001 | |
Culture |
| |
Name | Source | |
Phytophthora agathidicida NZFS 3770 | Scion* |
*Also deposited in the International Collection of Microorganisms as ICMP 17027.
","patternDescription":"Phytophthora agathidicida is the causal agent of kauri dieback disease in New Zealand. Sensitive and reliable detection of this plant pathogen is vital for effective disease management. Traditional detection methods rely on soil baiting followed by morphological identification (Beever et al., 2010; Tiakina Kauri, 2023). In 2020, a hybrid baiting/loop-mediated isothermal amplification (LAMP) assay was reported that applies LAMP directly to bait material, offering a faster alternative to culturing (Winkworth et al., 2020). The original assay was optimised and validated using OptiGene Isothermal Master Mix on a dedicated LAMP instrument (BioRanger, Diagenetix Inc.), reporting a limit of detection of 1 fg of total P. agathidicida DNA.
We initially explored using the P. agathidicida LAMP primers as part of a colorimetric, field-friendly workflow designed to couple with our oospore DNA extraction method (Palmer & Gerth, 2025; Palmer et al., 2025). Initial testing yielded poor sensitivity, which was not unexpected given that colorimetric readouts can exhibit reduced sensitivity relative to fluorometric detection (Aglietti et al., 2024). To investigate further, we re-examined the baseline assay performance in the literature. While an analytical sensitivity of 1 fg was reported in the text, the published amplification plots presented data down to 2 pg (2,000 fg; Winkworth et al., 2020). To clarify performance at lower concentrations, we undertook a study to directly assess the assay's limit of detection under real-time fluorescent conditions.
We attempted to replicate the reported conditions as closely as possible, using the same master mix (OptiGene Isothermal Master Mix), reported primer concentrations (F3/B3 and FIP/BIP), and incubation temperature (63 °C) as the original study (Winkworth et al., 2020). The published protocol did not report Loop F/Loop B primer concentrations, so we used the OptiGene manufacturer-recommended 0.4 µM final concentration (OptiGene. LAMP User Guide – Assay Design & Primers. https://www.optigene.co.uk/wp-content/uploads/2012/06/OptiGene-LAMP-User-Guide-Assay-Design-Primers-1.pdf). We did not have access to a BioRanger instrument, as Diagenetix, Inc. ceased operations in 2023 (PitchBook. 2026. Diagenetix company profile. https://pitchbook.com/profiles/company/112919-32). Instead, we used a QuantStudio 3 Real-Time PCR System (Applied Biosystems). While there is precedent in the literature for using real-time PCR platforms for LAMP fluorescence detection (García-Bernalt Diego et al., 2022; Stehlíková et al., 2020), instrument hardware was a primary variable differing from the original protocol. In a second experimental condition, we trialled NEB WarmStart Fluorescent LAMP Master Mix at its recommended incubation temperature (65 °C), maintaining the 0.4 µM Loop F/Loop B primer concentration in line with standard NEB guidelines (New England Biolabs. WarmStart Multi-Purpose LAMP/RT-LAMP 2X Master Mix with UDG protocol. https://www.neb.com/en-nz/protocols/warmstart-multi-purpose-lamp-rt-lamp-2x-master-mix-with-udg-protocol-neb-m1078). Reaction parameters (including primer ratios and incubation temperatures) were not independently re-optimised for either master mix on the QuantStudio platform; assay re-optimisation could plausibly improve performance, but was outside the scope of the present study.
No amplification was observed for either master mix at 1 fg or 10 fg. At 100 fg, amplification was variable: all OptiGene replicates produced a signal, but with high variability in take-off time and curve morphology, and one of three OptiGene no-template control (NTC) replicates showed both elevated initial background fluorescence and a non-specific fluorescence increase beginning at approximately 35 minutes (Figure 1A). This anomaly was specific to the OptiGene mix and was not observed with the NEB mix on the same QuantStudio 3 platform; we therefore cannot exclude a chemistry-specific artefact as a contributor to the variability seen at 100 fg with the OptiGene mix, which complicates interpretation of these particular data. With the NEB mix, only one of three 100 fg replicates amplified, while NTCs remained at baseline in all three replicates (Figure 1B). Both master mixes yielded robust, uniform sigmoidal curves at 1,000 fg.
Overall, under the experimental conditions tested here, we established a reliable detection limit of 1,000 fg for the P. agathidicida LAMP assay. We acknowledge that our study does not represent a direct, same-methods replication, which would require the original BioRanger instrument and exact original protocol. Instead, it evaluates assay reproducibility and robustness (Schloss, 2018), testing whether reported performance holds across alternative platforms and/or reagents. Although this LAMP assay remains officially approved for kauri dieback surveillance (Tiakina Kauri, 2023), the commercial unavailability of the BioRanger means operationalising it today inevitably requires platform adaptation. To date, no public inter-laboratory validation data exist to support such platform substitutions — a notable gap given that formal diagnostic validation frameworks treat multi-laboratory, multi-platform transferability as an essential tier for decentralised deployment (Tier 3; Cardwell et al., 2018; Groth-Helms et al., 2023). One report (Tomscha, 2026) notes an in-house comparison by the Ministry for Primary Industries’ Plant Health and Environment Laboratory that found a TaqMan qPCR assay (Than et al., 2013) to be more sensitive than the LAMP assay, without disclosing the obtained detection limits, methods or equipment used.
While these findings should not be construed as a failure of the original protocol under its specific conditions, they suggest that the assay's sensitivity is potentially not robust to platform or reagent substitution. Laboratories intending to deploy this approved workflow on alternative instruments should independently verify and re-optimise assay performance prior to relying on it for biosecurity decision-making.
","references":[{"reference":"Aglietti C, Benigno A, Cacciola SO, Moricca S. 2024. LAMP Reaction in Plant Disease Surveillance: Applications, Challenges, and Future Perspectives. Life 14: 1549.
","pubmedId":"","doi":"10.3390/life14121549"},{"reference":"Beever RE, Bellgard SE, Dick MA, Horner IJ, & Ramsfield TD. 2010. Detection of Phytophthora taxon Agathis (PTA). Landcare Research Report prepared for the Ministry for Agriculture & Forestry, Biosecurity New Zealand (on behalf of Kauri Dieback Joint Agency). https://perma.cc/2RKJ-GMDG
","pubmedId":"","doi":""},{"reference":"Cardwell K, Dennis G, Flannery AR, Fletcher J, Luster D, Nakhla M, et al., Levy. 2018. Principles of Diagnostic Assay Validation for Plant Pathogens: A Basic Review of Concepts. Plant Health Progress 19: 272-278.
","pubmedId":"","doi":"10.1094/PHP-06-18-0036-RV"},{"reference":"García-Bernalt Diego J, Fernández-Soto P, Márquez-Sánchez S, Santos Santos D, Febrer-Sendra B, Crego-Vicente B, et al., Muro. 2022. SMART-LAMP: A Smartphone-Operated Handheld Device for Real-Time Colorimetric Point-of-Care Diagnosis of Infectious Diseases via Loop-Mediated Isothermal Amplification. Biosensors 12: 424.
","pubmedId":"","doi":"10.3390/bios12060424"},{"reference":"Groth-Helms D, Rivera Y, Martin FN, Arif M, Sharma P, Castlebury LA. 2023. Terminology and Guidelines for Diagnostic Assay Development and Validation: Best Practices for Molecular Tests. PhytoFrontiers 3: 23-35.
","pubmedId":"","doi":"10.1094/PHYTOFR-05-22-0059-FI"},{"reference":"Palmer JTT, Gerth ML. 2025. A Method for the Separation of Phytophthora Oospores from Soil for DNA-Based Detection. Methods in Molecular Biology, Phytophthora. 2892:139-149.
","pubmedId":"","doi":"10.1007/978-1-0716-4330-3_10"},{"reference":"Palmer JT, Vink JN, Castro LM, Craig OJ, Davison EE, Gerth ML. 2025. Improved isolation and PCR detection of Phytophthora agathidicida oospores from soils. Microbiol Spectr 13(5): e0013525.
","pubmedId":"40197128","doi":""},{"reference":"Schloss PD. 2018. Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research. mBio 9(3):e00525-18. PMID: 29871915
","pubmedId":"","doi":"10.1128/mBio.00525-18"},{"reference":"Stehlíková D, Beran P, Cohen SP, Čurn V. 2020. Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 8: 1301.
","pubmedId":"32858943","doi":"10.3390/microorganisms8091301"},{"reference":"Than DJ, Hughes KJD, Boonhan N, Tomlinson JA, Woodhall JW, Bellgard SE. 2013. A TaqMan real‐time PCR assay for the detection of Phytophthora ‘taxon Agathis’ in soil, pathogen of Kauri in New Zealand. Forest Pathology 43: 324-330.
","pubmedId":"","doi":"10.1111/efp.12034"},{"reference":"Tiakina Kauri. 2023. Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https://perma.cc/ZV9N-AHWU
","pubmedId":"","doi":""},{"reference":"Tomscha S. 2026. Approval of qPCR - A TaqMan real-time PCR (Than et al. 2013) for use in P. agathidicida surveillance and diagnostics. Tiakina Kauri, Ministry for Primary Industries. https://perma.cc/9CSD-9YVE
","pubmedId":"","doi":""},{"reference":"Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. 2020. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLOS ONE 15: e0224007.
","pubmedId":"","doi":"10.1371/journal.pone.0224007"}],"title":"The limit of detection of a Phytophthora agathidicida LAMP assay is higher under alternative laboratory conditions
","reviews":[],"curatorReviews":[]},{"id":"464a960d-9549-4aa5-8b2b-baece48c7a58","decision":"publish","abstract":"Surveillance of Phytophthora agathidicida, the causal agent of kauri dieback, has included soil baiting followed by loop-mediated isothermal amplification (LAMP)-based detection. This approved assay was reported to detect 1 fg of DNA using OptiGene Isothermal Master Mix on a BioRanger instrument. We evaluated its analytical robustness using the same master mix on an alternative platform (QuantStudio 3), and separately tested an alternative NEB master mix. Both assays yielded a reliable detection limit of 1,000 fg, with variable detection at 100 fg and none below. Diagnostic laboratories should verify assay performance under their operational conditions prior to implementation.
","acknowledgements":"","authors":[{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","investigation","writing_originalDraft"],"email":"jade.palmer@vuw.ac.nz","firstName":"Jade TT","lastName":"Palmer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-6779-7638"},{"affiliations":["Victoria University of Wellington, New Zealand"],"departments":["School of Biological Sciences"],"credit":["conceptualization","project","resources","supervision","writing_reviewEditing"],"email":"monica.gerth@vuw.ac.nz","firstName":"Monica L","lastName":"Gerth","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-7959-7852"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Jade Palmer gratefully acknowledges PhD scholarship support from Victoria University of Wellington, Tiakina Kauri, the New Zealand Plant Protection Society, and Te Roroa Iwi.
","image":{"url":"https://portal.micropublication.org/uploads/9548ad527616aa6cdafe942ebcacfab3.jpg"},"imageCaption":"Amplification plots showing raw fluorescence over a 50-minute incubation. For each master mix, an independent 10-fold serial dilution of P. agathidicida genomic DNA (100,000 fg to 1 fg) was tested in technical triplicate (n=3). (A) OptiGene Isothermal Master Mix. (B) NEB WarmStart Fluorescent LAMP Master Mix. Coloured lines represent the dilution series; the black dashed line represents the no-template control (ntc).
","imageTitle":"Comparison of P. agathidicida LAMP assay sensitivity and reproducibility across two master mixes
","methods":"DNA Extraction and Quantification
Genomic DNA was extracted from P. agathidicida strain NZFS 3770 mycelial mats grown in potato dextrose broth (Difco). Mats were grown until they covered approximately 50% of the surface of a 90 mm Petri dish. Harvested mats were rinsed with sterile water, blotted dry, and ground to a fine powder in liquid nitrogen. Total genomic DNA was extracted using the DNeasy Plant Mini kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen). For each assay, a fresh 10-fold serial dilution series (100,000 fg to 1 fg) was prepared in sterile PCR-grade water.
Primer Preparation
The primer sequences used in this study were originally described by (Winkworth et al., 2020) for the molecular detection of P. agathidicida. The lyophilised primers (Macrogen, Korea) were resuspended in low-EDTA TE buffer (10 mM Tris-HCl, 0.1 mM EDTA) to a stock concentration of 100 µM and stored at -20 °C. Working concentrations are provided in the Reagents section below.
LAMP Assay Conditions and Data Analysis
Two reagent master mixes were evaluated: the original OptiGene Isothermal Master Mix and the WarmStart Fluorescent LAMP Kit (with UDG; NEB). Each LAMP master mix was evaluated in triplicate, including a no-template control (NTC) using sterile PCR-grade water in place of genomic DNA for every run. The originally reported OptiGene Isothermal Master Mix was used in 20 µL reactions incubated at 63 °C for 50 min. The alternative master mix, WarmStart Fluorescent LAMP Kit, was used in 25 µL reactions incubated at 65 °C for 50 min. All reactions were performed on a QuantStudio 3 Real-Time PCR System (Applied Biosystems) with fluorescence readings acquired every minute. Data were plotted and analysed using GraphPad Prism (v 11.0.0).
","reagents":"Primers | ||
Name | Sequence (5′ - 3′) | Final Concentration |
PTAF3 | TTATTTGAACCAACCTCATGT | 0.2 μM |
PTAB3 | TGTTTTACCTTGGGGACAA | 0.2 μM |
PTAFIP | GCTGTAGATAATCCAACTTTAAATCGTTTTGGTGTATTAATACGACCCCTAC | 0.6 μM |
PTABIP | CCACCCCATAGCCAATCAACAATATTTTGGGGTGCAACTGTT | 0.6 μM |
PTALF | TTAGTTTACATTTTACTTTTCCTTTTG | 0.4 μM |
PTALB | CCTATTAAAGGTATTGCAGAAAATAA | 0.4 μM |
Kits and Reagents | ||
Name (Supplier) | Catalogue Number | |
DNeasy Plant Mini kit (Qiagen) | 69104 | |
Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) | Q32854 | |
WarmStart Fluorescent LAMP Kit with UDG (New England Biolabs) | E1708 | |
Isothermal Master Mix (OptiGene) | ISO-DR001 | |
Culture |
| |
Name | Source | |
Phytophthora agathidicida NZFS 3770 | Scion* |
*Also deposited in the International Collection of Microorganisms as ICMP 17027.
","patternDescription":"Phytophthora agathidicida is the causal agent of kauri dieback disease in New Zealand. Sensitive and reliable detection of this plant pathogen is vital for effective disease management. Traditional detection methods rely on soil baiting followed by morphological identification (Beever et al., 2010; Tiakina Kauri, 2023). In 2020, a hybrid baiting/loop-mediated isothermal amplification (LAMP) assay was reported that applies LAMP directly to bait material, offering a faster alternative to culturing (Winkworth et al., 2020). The original assay was optimised and validated using OptiGene Isothermal Master Mix on a dedicated LAMP instrument (BioRanger, Diagenetix Inc.), reporting a limit of detection of 1 fg of total P. agathidicida DNA.
We initially explored using the P. agathidicida LAMP primers as part of a colorimetric, field-friendly workflow designed to couple with our oospore DNA extraction method (Palmer & Gerth, 2025; Palmer et al., 2025). Initial testing yielded poor sensitivity, which was not unexpected given that colorimetric readouts can exhibit reduced sensitivity relative to fluorometric detection (Aglietti et al., 2024). To investigate further, we re-examined the baseline assay performance in the literature. While an analytical sensitivity of 1 fg was reported in the text, the published amplification plots presented data down to 2 pg (2,000 fg; Winkworth et al., 2020). To clarify performance at lower concentrations, we undertook a study to directly assess the assay's limit of detection under real-time fluorescent conditions.
We attempted to replicate the reported conditions as closely as possible, using the same master mix (OptiGene Isothermal Master Mix), reported primer concentrations (F3/B3 and FIP/BIP), and incubation temperature (63 °C) as the original study (Winkworth et al., 2020). The published protocol did not report Loop F/Loop B primer concentrations, so we used the OptiGene manufacturer-recommended 0.4 µM final concentration (OptiGene. LAMP User Guide – Assay Design & Primers. https://www.optigene.co.uk/wp-content/uploads/2012/06/OptiGene-LAMP-User-Guide-Assay-Design-Primers-1.pdf). We did not have access to a BioRanger instrument, as Diagenetix, Inc. ceased operations in 2023 (PitchBook. 2026. Diagenetix company profile. https://pitchbook.com/profiles/company/112919-32). Instead, we used a QuantStudio 3 Real-Time PCR System (Applied Biosystems). While there is precedent in the literature for using real-time PCR platforms for LAMP fluorescence detection (García-Bernalt Diego et al., 2022; Stehlíková et al., 2020), instrument hardware was a primary variable differing from the original protocol. In a second experimental condition, we trialled NEB WarmStart Fluorescent LAMP Master Mix at its recommended incubation temperature (65 °C), maintaining the 0.4 µM Loop F/Loop B primer concentration in line with standard NEB guidelines (New England Biolabs. WarmStart Multi-Purpose LAMP/RT-LAMP 2X Master Mix with UDG protocol. https://www.neb.com/en-nz/protocols/warmstart-multi-purpose-lamp-rt-lamp-2x-master-mix-with-udg-protocol-neb-m1078). Reaction parameters (including primer ratios and incubation temperatures) were not independently re-optimised for either master mix on the QuantStudio platform; assay re-optimisation could plausibly improve performance, but was outside the scope of the present study.
No amplification was observed for either master mix at 1 fg or 10 fg. At 100 fg, amplification was variable: all OptiGene replicates produced a signal, but with high variability in take-off time and curve morphology, and one of three OptiGene no-template control (NTC) replicates showed both elevated initial background fluorescence and a non-specific fluorescence increase beginning at approximately 35 minutes (Figure 1A). This anomaly was specific to the OptiGene mix and was not observed with the NEB mix on the same QuantStudio 3 platform; we therefore cannot exclude a chemistry-specific artefact as a contributor to the variability seen at 100 fg with the OptiGene mix, which complicates interpretation of these particular data. With the NEB mix, only one of three 100 fg replicates amplified, while NTCs remained at baseline in all three replicates (Figure 1B). Both master mixes yielded robust, uniform sigmoidal curves at 1,000 fg.
Overall, under the experimental conditions tested here, we established a reliable detection limit of 1,000 fg for the P. agathidicida LAMP assay. We acknowledge that our study does not represent a direct, same-methods replication, which would require the original BioRanger instrument and exact original protocol. Instead, it evaluates assay reproducibility and robustness (Schloss, 2018), testing whether reported performance holds across alternative platforms and/or reagents. Although this LAMP assay remains officially approved for kauri dieback surveillance (Tiakina Kauri, 2023), the commercial unavailability of the BioRanger means operationalising it today inevitably requires platform adaptation. To date, no public inter-laboratory validation data exist to support such platform substitutions — a notable gap given that formal diagnostic validation frameworks treat multi-laboratory, multi-platform transferability as an essential tier for decentralised deployment (Tier 3; Cardwell et al., 2018; Groth-Helms et al., 2023). One report (Tomscha, 2026) notes an in-house comparison by the Ministry for Primary Industries’ Plant Health and Environment Laboratory that found a TaqMan qPCR assay (Than et al., 2013) to be more sensitive than the LAMP assay, without disclosing the obtained detection limits, methods or equipment used.
While these findings should not be construed as a failure of the original protocol under its specific conditions, they suggest that the assay's sensitivity is potentially not robust to platform or reagent substitution. Laboratories intending to deploy this approved workflow on alternative instruments should independently verify and re-optimise assay performance prior to relying on it for biosecurity decision-making.
","references":[{"reference":"Aglietti C, Benigno A, Cacciola SO, Moricca S. 2024. LAMP Reaction in Plant Disease Surveillance: Applications, Challenges, and Future Perspectives. Life 14: 1549.
","pubmedId":"","doi":"10.3390/life14121549"},{"reference":"Beever RE, Bellgard SE, Dick MA, Horner IJ, & Ramsfield TD. 2010. Detection of Phytophthora taxon Agathis (PTA). Landcare Research Report prepared for the Ministry for Agriculture & Forestry, Biosecurity New Zealand (on behalf of Kauri Dieback Joint Agency). https://perma.cc/2RKJ-GMDG
","pubmedId":"","doi":""},{"reference":"Cardwell K, Dennis G, Flannery AR, Fletcher J, Luster D, Nakhla M, et al., Levy. 2018. Principles of Diagnostic Assay Validation for Plant Pathogens: A Basic Review of Concepts. Plant Health Progress 19: 272-278.
","pubmedId":"","doi":"10.1094/PHP-06-18-0036-RV"},{"reference":"García-Bernalt Diego J, Fernández-Soto P, Márquez-Sánchez S, Santos Santos D, Febrer-Sendra B, Crego-Vicente B, et al., Muro. 2022. SMART-LAMP: A Smartphone-Operated Handheld Device for Real-Time Colorimetric Point-of-Care Diagnosis of Infectious Diseases via Loop-Mediated Isothermal Amplification. Biosensors 12: 424.
","pubmedId":"","doi":"10.3390/bios12060424"},{"reference":"Groth-Helms D, Rivera Y, Martin FN, Arif M, Sharma P, Castlebury LA. 2023. Terminology and Guidelines for Diagnostic Assay Development and Validation: Best Practices for Molecular Tests. PhytoFrontiers 3: 23-35.
","pubmedId":"","doi":"10.1094/PHYTOFR-05-22-0059-FI"},{"reference":"Palmer JTT, Gerth ML. 2025. A Method for the Separation of Phytophthora Oospores from Soil for DNA-Based Detection. Methods in Molecular Biology, Phytophthora. 2892:139-149.
","pubmedId":"","doi":"10.1007/978-1-0716-4330-3_10"},{"reference":"Palmer JT, Vink JN, Castro LM, Craig OJ, Davison EE, Gerth ML. 2025. Improved isolation and PCR detection of Phytophthora agathidicida oospores from soils. Microbiol Spectr 13(5): e0013525.
","pubmedId":"40197128","doi":""},{"reference":"Schloss PD. 2018. Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research. mBio 9(3):e00525-18. PMID: 29871915
","pubmedId":"","doi":"10.1128/mBio.00525-18"},{"reference":"Stehlíková D, Beran P, Cohen SP, Čurn V. 2020. Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 8: 1301.
","pubmedId":"32858943","doi":"10.3390/microorganisms8091301"},{"reference":"Than DJ, Hughes KJD, Boonhan N, Tomlinson JA, Woodhall JW, Bellgard SE. 2013. A TaqMan real‐time PCR assay for the detection of Phytophthora ‘taxon Agathis’ in soil, pathogen of Kauri in New Zealand. Forest Pathology 43: 324-330.
","pubmedId":"","doi":"10.1111/efp.12034"},{"reference":"Tiakina Kauri. 2023. Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https://perma.cc/ZV9N-AHWU
","pubmedId":"","doi":""},{"reference":"Tomscha S. 2026. Approval of qPCR - A TaqMan real-time PCR (Than et al. 2013) for use in P. agathidicida surveillance and diagnostics. Tiakina Kauri, Ministry for Primary Industries. https://perma.cc/9CSD-9YVE
","pubmedId":"","doi":""},{"reference":"Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. 2020. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLOS ONE 15: e0224007.
","pubmedId":"","doi":"10.1371/journal.pone.0224007"}],"title":"The limit of detection of a Phytophthora agathidicida LAMP assay is higher under alternative laboratory conditions
","reviews":[],"curatorReviews":[]}]}},"species":{"species":[{"value":"acer saccharum","label":"Acer saccharum","imageSrc":"","imageAlt":"","mod":"TreeGenes","modLink":"https://treegenesdb.org","linkVariable":""},{"value":"achillea millefolium","label":"Achillea millefolium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"acinetobacter baylyi","label":"Acinetobacter baylyi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"actinobacteria bacterium","label":"Actinobacteria bacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adelges tsugae","label":"Adelges tsugae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adenocaulon chilense","label":"Adenocaulon chilense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aedes japonicus","label":"Aedes japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aegorhinus vitulus","label":"Aegorhinus vitulus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aerococcus","label":"Aerococcus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alaimidae","label":"Alaimidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"allobates femoralis","label":"Allobates femoralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alnus glutinosa","label":"Alnus glutinosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa aestivalis","label":"Alosa aestivalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa pseudoharengus","label":"Alosa pseudoharengus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alternaria alternata","label":"Alternaria alternata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"amynthas agrestis","label":"Amynthas Agrestis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma caninum","label":"Ancylostoma caninum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma ceylanicum","label":"Ancylostoma ceylanicum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anemone multifida","label":"Anemone multifida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anguilla rostrata","label":"Anguilla rostrata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anisakis simplex","label":"Anisakis simplex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anomala albopilosa","label":"Anomala albopilosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arabidopsis","label":"Arabidopsis","imageSrc":"arabidopsis.png","imageAlt":"Arabidopsis graphic by Zoe Zorn CC BY 4.0","mod":"TAIR","modLink":"https://arabidopsis.org","linkVariable":""},{"value":"architeuthis dux","label":"Architeuthis dux","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arion vulgaris","label":"Arion vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"armeria","label":"Armeria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"artemia","label":"Artemia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arthrobacter sp.","label":"Arthrobacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia","label":"Ascaridia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia galli","label":"Ascaridia galli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"asparagopsis taxiformis","label":"Asparagopsis taxiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"astatotilapia burtoni","label":"Astatotilapia burtoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"avena sativa","label":"Avena sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aves","label":"Aves","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus","label":"Bacillus (firmicutes)","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus cereus","label":"Bacillus cereus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus mycoides","label":"Bacillus mycoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus subtilis","label":"Bacillus subtilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus thuringiensis","label":"Bacillus thuringiensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus toyonensis","label":"Bacillus toyonensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus wiedmannii","label":"Bacillus wiedmannii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteria","label":"Bacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteriophage","label":"Bacteriophage","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bactrocera","label":"Bactrocera sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"batrachospermum gelatinosum","label":"Batrachospermum gelatinosum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula lenta","label":"Betula lenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula nigra","label":"Betula nigra","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus dahlbohmii","label":"Bombus dahlbohmii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus terrestris","label":"Bombus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombyx mori","label":"Bombyx mori","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bos taurus","label":"Bos Taurus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brachygobius doriae","label":"Brachygobius doriae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica oleracea","label":"Brassica oleracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica rapa","label":"Brassica rapa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brugia malayi","label":"Brugia malayi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"burkholderia thailandensis","label":"Burkholderia thailandensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"buttiauxella","label":"Buttiauxella","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis brenneri","label":"Caenorhabditis brenneri","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis briggsae","label":"Caenorhabditis briggsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"c. elegans","label":"Caenorhabditis elegans","imageSrc":"c-elegans.jpg","imageAlt":"C. elegans graphic by Zoe Zorn CC BY 4.0","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"caenorhabditis inopinata","label":"Caenorhabditis inopinata","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis japonica","label":"Caenorhabditis japonica","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis nigoni","label":"Caenorhabditis nigoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis remanei","label":"Caenorhabditis remanei","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis tropicalis","label":"Caenorhabditis tropicalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus","label":"Calidifontibacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus erzuremensis","label":"Calidifontibacillus erzuremensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calliphora sp","label":"Calliphora sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caltha sagittata","label":"Caltha sagittata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cambarus latimanus","label":"Cambarus latimanus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"candida albicans","label":"Candida albicans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"canis familiaris","label":"Canis familiaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cannabis sativa","label":"Cannabis sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caretta caretta","label":"Caretta caretta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cassiopea xamachana","label":"Cassiopea xamachana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caulobacter vibrioides","label":"Caulobacter vibrioides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cephalopods","label":"Cephalopoda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cerastium arvense","label":"Cerastium arvense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceriodaphnia","label":"Ceriodaphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceroglossus suturalis","label":"Ceroglossus suturalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chaetoceros","label":"Chaetoceros","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chamaecrista fasciculata","label":"Chamaecrista fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chilicola chalcidiformis","label":"Chilicola chalcidiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chitinimonas","label":"Chitinimonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chlamydomonas reinhardtii","label":"Chlamydomonas reinhardtii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chromobacterium","label":"Chromobacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysemys picta","label":"Chrysemys picta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysoperla rufilabris","label":"Chrysoperla rufilabris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"citrus","label":"Citrus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"clavibacter sp.","label":"Clavibacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"colinus virginianus","label":"Colinus virginianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crassostrea virginica","label":"Crassostrea virginica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crithidia fasciculata","label":"Crithidia fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cutibacterium acnes","label":"Cutibacterium acnes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cyanobacteria","label":"Cyanobacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia","label":"Daphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia pulex","label":"Daphnia pulex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dermacoccus nishinomiyaensis","label":"Dermacoccus nishinomiyaensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera","label":"Diabrotica virgifera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera virgifera virus 1","label":"Diabrotica virgifera virgifera virus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"d. discoideum","label":"Dictyostelium discoideum","imageSrc":"dicty.png","imageAlt":"D. discoideum","mod":"dictyBase","modLink":"http://dictybase.org","linkVariable":""},{"value":"diptera","label":"Diptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dotocryptus bellicosus","label":"Dotocryptus bellicosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drechmeria coniospora","label":"Drechmeria coniospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drosophila","label":"Drosophila","imageSrc":"drosophila.png","imageAlt":"Drosophila graphic by Zoe Zorn CC BY 4.0","mod":"FlyBase","modLink":"https://flybase.org/doi/","linkVariable":"doi"},{"value":"dryopteris campyloptera","label":"Dryopteris campyloptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris expansa","label":"Dryopteris expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris intermedia","label":"Dryopteris intermedia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dugesia dorotocephala","label":"Dugesia dorotocephala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"elasmobranchii","label":"Elasmobranchii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"embryophyta","label":"Embryophyta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enoploteuthis chunii","label":"Enoploteuthis chunii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterobacter aerogenes","label":"Enterobacter aerogenes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterococcus raffinosus","label":"Enterococcus raffinosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"epichloë coenophiala","label":"Epichloë coenophiala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"equus caballus","label":"Equus caballus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erigeron sp","label":"Erigeron sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eristalis","label":"Eristalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eruca vesicaria","label":"Eruca vesicaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erwinia carotovora","label":"Erwinia carotovora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erythronium americanum","label":"Erythronium americanum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"escherichia coli","label":"Escherichia coli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eukaryota","label":"Eukaryotes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"felis catus","label":"Felis catus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella novicida","label":"Francisella novicida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella tularensis","label":"Francisella tularensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fraxinus americana","label":"Fraxinus americana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fucus distichus","label":"Fucus distichus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fungi","label":"Fungi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gasteropelecus sp.","label":"Gasteropelecus sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"geranium sp","label":"Geranium sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"girardia","label":"Girardia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glaucomys volans","label":"Glaucomys volans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glycine max","label":"Glycine max","imageSrc":"","imageAlt":"","mod":"Soybase","modLink":"https://soybase.org","linkVariable":""},{"value":"glyptemys insculpta","label":"Glyptemys insculpta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gossypium hirsutum","label":"Gossypium hirsutum","imageSrc":"","imageAlt":"","mod":"CottonGen","modLink":"https://www.cottongen.org/","linkVariable":""},{"value":"gromphadorhina portentosa","label":"Gromphadorhina portentosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gryllodes sigillatus","label":"Gryllodes sigillatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"haliotis rufescens","label":"Haliotis rufescens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hepacivirus hominis","label":"Hepatitis C Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"herpes simplex virus type 1","label":"Herpes simplex virus type 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human","label":"Human","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human coronavirus oc43","label":"Human coronavirus OC43","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydra vulgaris","label":"Hydra vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydropsyche sp","label":"Hydropsyche sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hymenoptera","label":"Hymenoptera","imageSrc":"","imageAlt":"","mod":"Hymenoptera Genome Database","modLink":"https://hymenoptera.elsiklab.missouri.edu/","linkVariable":""},{"value":"hypochaeris radicata","label":"Hypochaeris radicata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hypodynerus vespiformis","label":"Hypodynerus vespiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflaviridae","label":"Iflaviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflavuris","label":"Iflavirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ipomoea hederacea","label":"Ipomoea hederacea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera","label":"Ischnomera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera ruficollis","label":"Ischnomera ruficollis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"julidochromis marlieri","label":"Julidochromis marlieri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"juniperus virginiana","label":"Juniperus virginiana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"kluyveromyces marxianus","label":"Kluyveromyces marxianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"l. casei","label":"L. casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lacticaseibacillus casei","label":"Lacticaseibacillus casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lactobacillus","label":"Lactobacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"larentiinae sp","label":"Larentiinae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"laurus nobilis","label":"Laurus nobilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lepidoptera","label":"Lepidoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"leucanthemum vulgare","label":"Leucanthemum vulgare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ligilactobacillus","label":"Ligilactobacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ligilactobacillus salivarius","label":"Ligilactobacillus salivarius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"limosilactobacillus","label":"Limosilactobacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"linepithema humile","label":"Linepithema humile","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"liometopum occidentale","label":"Liometopum occidentale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lolium arundinaceum","label":"Lolium arundinaceum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lontra longicaudis","label":"Lontra longicaudis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbriculus variegatus","label":"Lumbriculus variegatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbricus terrestris","label":"Lumbricus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lupinus polyphyllus","label":"Lupinus polyphyllus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lycorma delicatula","label":"Lycorma delicatula","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lynx rufus","label":"Lynx rufus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"magnaporthe oryzae","label":"Magnaporthe oryzae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mammalia","label":"Mammalia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"manihot esculenta","label":"Manihot esculenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"medicago lupulina","label":"Medicago lupulina","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"meloidogyne","label":"Meloidogyne","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mimus polyglottos","label":"Mimus polyglottos","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bryophyta","label":"Mosses","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mouse","label":"Mouse","imageSrc":"","imageAlt":"","mod":"MGI","modLink":"https://informatics.jax.org","linkVariable":""},{"value":"m. minutoides","label":"Mus minutoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mycobacterium smegmatis","label":"Mycobacterium smegmatis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nakaseomyces glabratus","label":"Nakaseomyces glabratus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nauphoeta cinerea","label":"Nauphoeta cinerea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"neurospora","label":"Neurospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"n. benthamiana","label":"Nicotiana benthamiana","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/Nicotiana_benthamiana/genome","linkVariable":""},{"value":"nicotiana tabacum","label":"Nicotiana tabacum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae","label":"Noctuidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae sp","label":"Noctuidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nothobranchius furzeri","label":"Nothobranchius furzeri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"onchocerca volvulus","label":"Onchocerca volvulus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"orconectes virilis","label":"Orconectes virilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ormia ochracea","label":"Ormia ochracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"o. sativa","label":"Oryza sativa","imageSrc":"","imageAlt":"","mod":"Gramene","modLink":"https://www.gramene.org/","linkVariable":""},{"value":"other","label":"Other","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"oxalis enneaphylla","label":"Oxalis enneaphylla","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea","label":"Pantoea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea agglomerans","label":"Pantoea agglomerans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"papaver sp","label":"Papaver sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paramecium bursaria","label":"Paramecium bursaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"partitiviridae","label":"Partitiviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pelodiscus sinensis","label":"Pelodiscus sinensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"perezia recurvata","label":"Perezia recurvata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"petromyzon marinus","label":"Petromyzon marinus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis","label":"Photinus pyralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis associated partiti-like virus","label":"Photinus pyralis associated partiti-like virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis iflavirus 1","label":"Photinus pyralis iflavirus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"physcomitrium patens","label":"Physcomitrium patens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus strobus","label":"Pinus strobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus taeda","label":"Pinus taeda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"platycheirus","label":"Platycheirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"plectus sambesii","label":"Plectus sambesii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pogonomyrmex occidentalis","label":"Pogonomyrmex occidentalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"poncirus trifoliata","label":"Poncirus trifoliata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"populus deltoides","label":"Populus deltoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"potato virus y","label":"Potato virus Y","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"primula magellanica","label":"Primula magellanica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pristionchus pacificus","label":"Pristionchus pacificus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"prunus persica","label":"Prunus persica","imageSrc":"","imageAlt":"","mod":"Genome Database for Rosaceae","modLink":"https://www.rosaceae.org/","linkVariable":""},{"value":"psalmopoeus iriminia","label":"Psalmopoeus iriminia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudanabaena sp.","label":"Pseudanabaena sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas","label":"Pseudomonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas aeruginosa","label":"Pseudomonas aeruginosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas glycinae","label":"Pseudomonas glycinae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas putida","label":"Pseudomonas putida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas syringae","label":"Pseudomonas syringae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pterophyllum scalare","label":"Pterophyllum scalare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"python regius","label":"Python regius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"quercus macrocarpa","label":"Quercus macrocarpa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ralstonia solanacearum","label":"Ralstonia solanacearum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranitomeya imitator","label":"Ranitomeya imitator","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranunculus peduncularis","label":"Ranunculus peduncularis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"rat","label":"Rat","imageSrc":"","imageAlt":"","mod":"RGD","modLink":"https://rgd.mcw.edu","linkVariable":""},{"value":"rheinheimera","label":"Rheinheimera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ribes rubrum","label":"Ribes rubrum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"sars-cov-2","label":"SARS-CoV-2","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. cerevisiae","label":"Saccharomyces cerevisiae","imageSrc":"yeast.png","imageAlt":"Yeast graphic by Zoe Zorn CC BY 4.0","mod":"SGD","modLink":"https://yeastgenome.org","linkVariable":""},{"value":"saccharomyces paradoxus","label":"Saccharomyces paradoxus ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. uvarum","label":"Saccharomyces uvarum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schistosoma","label":"Schistosoma","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schizosaccharomyces japonicus","label":"Schizosaccharomyces japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. pombe","label":"Schizosaccharomyces pombe","imageSrc":"pombe.png","imageAlt":"Pombe graphic by Zoe Zorn © Caltech","mod":"PomBase","modLink":"https://www.pombase.org/reference/PMID:","linkVariable":"pmId"},{"value":"schmidtea mediterranea","label":"Schmidtea mediterranea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"senecio sp","label":"Senecio sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"simocephalus","label":"Simocephalus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"siraitia grosvenorii","label":"Siraitia grosvenorii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"solanum lycopersicum","label":"Solanum lycopersicum","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/1/view/","linkVariable":""},{"value":"sorghum","label":"Sorghum","imageSrc":"","imageAlt":"","mod":"SorghumBase","modLink":"https://www.sorghumbase.org","linkVariable":""},{"value":"spiroplasma eriocheiris","label":"Spiroplasma eriocheiris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus aureus","label":"Staphylococcus aureus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus epidermidis","label":"Staphylococcus epidermidis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"steinernema carpocapsae","label":"Steinernema carpocapsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"steinernema hermaphroditum","label":"Steinernema hermaphroditum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stenotrophomonas geniculata","label":"Stenotrophomonas geniculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stewartia floidana","label":"Stewartia floridana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus gordonii ","label":"Streptococcus gordonii ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus mutans","label":"Streptococcus mutans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":" streptococcus pneumoniae","label":"Streptococcus pneumoniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. purpuratus","label":"Strongylocentrotus purpuratus","imageSrc":"","imageAlt":"","mod":"Echinobase","modLink":"https://www.echinobase.org","linkVariable":""},{"value":"strongyloides ratti","label":"Strongyloides ratti","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"sulfolobus","label":"Sulfolobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"symphoricarpos albus","label":"Symphoricarpos albus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syncirsodes","label":"Syncirsodes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"synechococcus elongatus","label":"Synechococcus elongatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syrphidae","label":"Syrphidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tarantobelus jeffdanielsi","label":"Tarantobelus jeffdanielsi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"taraxacum officinale","label":"Taraxacum officinale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tatochila theodice","label":"Tatochila theodice","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetrahymena","label":"Tetrahymena","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetramorium immigrans","label":"Tetramorium immigrans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tomato brown rugose fruit virus","label":"ToBRFV","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trachemys scripta","label":"Trachemys scripta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tribolium castaneum","label":"Tribolium castaneum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichoptera","label":"Trichoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichuris muris","label":"Trichuris muris","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"trifolium repens","label":"Trifolium repens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trypoxylus dichotomus","label":"Trypoxylus dichotomus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tsuga canadensis","label":"Tsuga canadensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ulva expansa","label":"Ulva expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"universal","label":"Universal","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"vargula hilgendorfii","label":"Vargula hilgendorfii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"vespula vulgaris","label":"Vespula vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"virus","label":"Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"watasenia scintillans","label":"Watasenia scintillans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"wolbachia pipientis","label":"Wolbachia pipientis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"xenopus","label":"Xenopus","imageSrc":"xenopus.png","imageAlt":"Xenopus graphic by Zoe Zorn CC BY 4.0","mod":"XenBase","modLink":"https://xenbase.org","linkVariable":""},{"value":"xenorhabdus griffiniae","label":"Xenorhabdus griffiniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"yramea cytheris","label":"Yramea cytheris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zaprionus indianus","label":"Zaprionus indianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zea mays","label":"Zea mays","imageSrc":"","imageAlt":"","mod":"MaizeGDB","modLink":"https://www.maizegdb.org","linkVariable":""},{"value":"zebrafish","label":"Zebrafish","imageSrc":"zebrafish.png","imageAlt":"Zebrafish graphic by Zoe Zorn CC BY 4.0","mod":"ZFIN","modLink":"https://zfin.org","linkVariable":""}]}},"pageContext":{"id":"e4b35212-946a-4c0e-ab40-38a0ae6d833a","citedBy":[],"parsedCsv":{"csvHeader":[],"csvData":[]}}}, "staticQueryHashes": ["2114697108"]}