Pub Date : 2024-07-01Epub Date: 2024-06-29DOI: 10.1094/PHYTO-01-24-0010-SC
Cristofer Motoche-Monar, Diego Andrade, Washington D Pijal, Francisco Hidrobo, Rolando Armas, Emily Sánchez-Real, Gabriela Rocha-Chauca, José A Castillo
Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of Ralstonia solanacearum species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the R. solanacearum, R. pseudosolanacearum, and R. syzygii strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.
{"title":"CRISPRals: A Web Database for Assessing the CRISPR Defense System in the <i>Ralstonia solanacearum</i> Species Complex to Avoid Phage Resistance.","authors":"Cristofer Motoche-Monar, Diego Andrade, Washington D Pijal, Francisco Hidrobo, Rolando Armas, Emily Sánchez-Real, Gabriela Rocha-Chauca, José A Castillo","doi":"10.1094/PHYTO-01-24-0010-SC","DOIUrl":"10.1094/PHYTO-01-24-0010-SC","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of <i>Ralstonia solanacearum</i> species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the <i>R. solanacearum</i>, <i>R. pseudosolanacearum</i>, and <i>R. syzygii</i> strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140013226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-06-29DOI: 10.1094/PHYTO-08-23-0287-R
Wen-Chi Hu, Jui-Chi Tsai, Hao-Wen Cheng, Chung-Hao Huang, Joseph A J Raja, Fang-Yu Chang, Chin-Chih Chen, Chu-Hui Chiang, Shyi-Dong Yeh
HC-Pro and coat protein (CP) genes of a potyvirus facilitate cell-to-cell movement and are involved in the systemic movement of the viruses. The interaction between HC-Pro and CP is mandatory for aphid transmission. Two turnip mosaic virus (TuMV) isolates, RC4 and YC5, were collected from calla lily plants in Taiwan. The virus derived from the infectious clone pYC5 cannot move systemically in Chenopodium quinoa plants and loses aphid transmissibility in Nicotiana benthamiana plants, like the initially isolated virus. Sequence analysis revealed that two amino acids, P5 and A206, of YC5 CP uniquely differ from RC4 and other TuMV strains. Recombination assay and site-directed mutagenesis revealed that the fifth residue of leucine (L) at the N-terminal region of the CP (TuMV-RC4), rather than proline (P) (TuMV-YC5), is critical to permit the systemic spread in C. quinoa plants. Moreover, the single substitution mutant YC5-CPP5L became aphid transmissible, similar to RC4. Fluorescence microscopy revealed that YC5-GFP was restricted in the petioles of inoculated leaves, whereas YC5-CPP5L-GFP translocated through the petioles of inoculated leaves, the main stem, and the petioles of the upper uninoculated leaves of C. quinoa plants. In addition, YC5-GUS was blocked at the basal part of the petiole connecting to the main stem of the inoculated C. quinoa plants, whereas YC5-CPP5L-GFP translocated to the upper leaves. Thus, a single amino acid, the residue L5 at the N-terminal region right before the 6DAG8 motif, is critical for the systemic translocation ability of TuMV in a local lesion host and for aphid transmissibility in a systemic host.
{"title":"The Fifth Residue of the Coat Protein of Turnip Mosaic Virus Is Responsible for Long-Distance Movement in a Local-Lesion Host and Aphid Transmissibility in a Systemic Host.","authors":"Wen-Chi Hu, Jui-Chi Tsai, Hao-Wen Cheng, Chung-Hao Huang, Joseph A J Raja, Fang-Yu Chang, Chin-Chih Chen, Chu-Hui Chiang, Shyi-Dong Yeh","doi":"10.1094/PHYTO-08-23-0287-R","DOIUrl":"10.1094/PHYTO-08-23-0287-R","url":null,"abstract":"<p><p>HC-Pro and coat protein (CP) genes of a potyvirus facilitate cell-to-cell movement and are involved in the systemic movement of the viruses. The interaction between HC-Pro and CP is mandatory for aphid transmission. Two turnip mosaic virus (TuMV) isolates, RC4 and YC5, were collected from calla lily plants in Taiwan. The virus derived from the infectious clone pYC5 cannot move systemically in <i>Chenopodium quinoa</i> plants and loses aphid transmissibility in <i>Nicotiana benthamiana</i> plants, like the initially isolated virus. Sequence analysis revealed that two amino acids, P<sub>5</sub> and A<sub>206</sub>, of YC5 CP uniquely differ from RC4 and other TuMV strains. Recombination assay and site-directed mutagenesis revealed that the fifth residue of leucine (L) at the N-terminal region of the CP (TuMV-RC4), rather than proline (P) (TuMV-YC5), is critical to permit the systemic spread in <i>C. quinoa</i> plants. Moreover, the single substitution mutant YC5-CP<sup>P5L</sup> became aphid transmissible, similar to RC4. Fluorescence microscopy revealed that YC5-GFP was restricted in the petioles of inoculated leaves, whereas YC5-CP<sup>P5L</sup>-GFP translocated through the petioles of inoculated leaves, the main stem, and the petioles of the upper uninoculated leaves of <i>C. quinoa</i> plants. In addition, YC5-GUS was blocked at the basal part of the petiole connecting to the main stem of the inoculated <i>C. quinoa</i> plants, whereas YC5-CP<sup>P5L</sup>-GFP translocated to the upper leaves. Thus, a single amino acid, the residue L<sub>5</sub> at the N-terminal region right before the <sup>6</sup>DAG<sup>8</sup> motif, is critical for the systemic translocation ability of TuMV in a local lesion host and for aphid transmissibility in a systemic host.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Transcription factors play critical roles in diverse biological processes in fungi. XlnR, identified as a transcriptional activator that regulates the expression of the extracellular xylanase genes in fungi, has not been extensively studied for its function in fungal development and pathogenicity in rice false smut fungus Ustilaginoidea virens. In this study, we characterized UvXlnR in U. virens and established that the full-length, N-terminal, and C-terminal forms have the ability to activate transcription. The study further demonstrated that UvXlnR plays crucial roles in various aspects of U. virens biology. Deletion of UvXlnR affected growth, conidiation, and stress response. UvXlnR mutants also exhibited reduced pathogenicity, which could be partially attributed to the reduced expression of xylanolytic genes and extracellular xylanase activity of U. virens during the infection process. Our results indicate that UvXlnR is involved in regulating growth, conidiation, stress response, and pathogenicity.
转录因子在真菌的各种生物过程中发挥着关键作用。XlnR 是一种转录激活因子,可调控真菌胞外木聚糖酶基因的表达,但它在水稻假烟真菌 Ustilaginoidea virens 的真菌发育和致病性中的功能尚未得到广泛研究。在这项研究中,我们对 U. virens 中的 UvXlnR 进行了表征,并确定 UvXlnR 的全长、N 端和 C 端形式具有激活转录的能力。研究进一步证明,UvXlnR 在 U. virens 生物学的各个方面发挥着关键作用。缺失 UvXlnR 会影响生长、分生孢子和应激反应。UvXlnR 突变体还表现出较低的致病性,其部分原因可能是在感染过程中,U. virens 的木聚糖分解基因表达和胞外木聚糖酶活性降低。我们的研究结果表明,UvXlnR 参与了生长、分生孢子、应激反应和致病性的调控。
{"title":"Transcriptional Activator UvXlnR Is Required for Conidiation and Pathogenicity of Rice False Smut Fungus <i>Ustilaginoidea virens</i>.","authors":"Jiali Yan, Rui Wang, Mengyao Wu, Minzheng Cai, Jinsong Qu, Lianmeng Liu, Jiatao Xie, Weixiao Yin, Chaoxi Luo","doi":"10.1094/PHYTO-01-24-0038-R","DOIUrl":"10.1094/PHYTO-01-24-0038-R","url":null,"abstract":"<p><p>Transcription factors play critical roles in diverse biological processes in fungi. XlnR, identified as a transcriptional activator that regulates the expression of the extracellular xylanase genes in fungi, has not been extensively studied for its function in fungal development and pathogenicity in rice false smut fungus <i>Ustilaginoidea virens</i>. In this study, we characterized <i>UvXlnR</i> in <i>U. virens</i> and established that the full-length, N-terminal, and C-terminal forms have the ability to activate transcription. The study further demonstrated that <i>UvXlnR</i> plays crucial roles in various aspects of <i>U. virens</i> biology. Deletion of <i>UvXlnR</i> affected growth, conidiation, and stress response. <i>UvXlnR</i> mutants also exhibited reduced pathogenicity, which could be partially attributed to the reduced expression of xylanolytic genes and extracellular xylanase activity of <i>U. virens</i> during the infection process. Our results indicate that <i>UvXlnR</i> is involved in regulating growth, conidiation, stress response, and pathogenicity.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140176125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1094/PHYTO-08-23-0286-R
Richard F Davis, Karen Harris-Shultz, Joseph E Knoll, Matthew Krakowsky, Brian Scully
This study provides the first report of a quantitative trait locus (QTL) in maize (Zea mays) for resistance to the southern root-knot nematode (SRKN) (Meloidogyne incognita). The SRKN can feed on the roots of maize in the U.S. Southern Coastal Plain region and can cause yield losses of 30% or more in heavily infested fields. Increases in SRKN density in the soil may reduce the yield for subsequently planted susceptible crops. The use of maize hybrids with resistance to SRKN could prevent an increase in SRKN density, yet no genetic regions have been identified that confer host resistance. In this study, a B73 (susceptible) × Ky21 (resistant) S5 recombinant inbred line (RIL) population was phenotyped for total number of eggs (TE) and root weight. This population had been genotyped using single-nucleotide polymorphisms (SNPs). By utilizing the SNP data with the phenotype data, a single QTL was identified on chromosome 5 that explained 15% of the phenotypic variation (PV) for the number of eggs and 11% of the PV for the number of eggs per gram of root (EGR). Plants that were homozygous for the Ky21 allele for the most associated marker PZA03172.3 had fewer eggs and fewer EGR than the plants that were homozygous or heterozygous for the B73 allele. Thus, the first QTL for SRKN resistance in maize has been identified and could be incorporated into maize hybrids.
{"title":"A Quantitative Trait Locus on Maize Chromosome 5 Is Associated with Root-Knot Nematode Resistance.","authors":"Richard F Davis, Karen Harris-Shultz, Joseph E Knoll, Matthew Krakowsky, Brian Scully","doi":"10.1094/PHYTO-08-23-0286-R","DOIUrl":"10.1094/PHYTO-08-23-0286-R","url":null,"abstract":"<p><p>This study provides the first report of a quantitative trait locus (QTL) in maize (<i>Zea mays</i>) for resistance to the southern root-knot nematode (SRKN) (<i>Meloidogyne incognita</i>). The SRKN can feed on the roots of maize in the U.S. Southern Coastal Plain region and can cause yield losses of 30% or more in heavily infested fields. Increases in SRKN density in the soil may reduce the yield for subsequently planted susceptible crops. The use of maize hybrids with resistance to SRKN could prevent an increase in SRKN density, yet no genetic regions have been identified that confer host resistance. In this study, a B73 (susceptible) × Ky21 (resistant) S<sub>5</sub> recombinant inbred line (RIL) population was phenotyped for total number of eggs (TE) and root weight. This population had been genotyped using single-nucleotide polymorphisms (SNPs). By utilizing the SNP data with the phenotype data, a single QTL was identified on chromosome 5 that explained 15% of the phenotypic variation (PV) for the number of eggs and 11% of the PV for the number of eggs per gram of root (EGR). Plants that were homozygous for the Ky21 allele for the most associated marker PZA03172.3 had fewer eggs and fewer EGR than the plants that were homozygous or heterozygous for the B73 allele. Thus, the first QTL for SRKN resistance in maize has been identified and could be incorporated into maize hybrids.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140013225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-07-02DOI: 10.1094/PHYTO-12-23-0507-R
Mana Ohkura, Bryan R Beck, Carolyn F Scagel, Jerry E Weiland
The fungal pathogen Calonectria pseudonaviculata causes boxwood blight and is a significant threat to the boxwood industry, as well as historic boxwood gardens. The pathogen produces conidia in sticky masses that are splash dispersed, which germinate and infect through stomata on the leaves or stems, causing leaf spots and stem lesions. Despite its ability to cause severe infections on boxwood plants, the pathogen often has a low germination rate on artificial media under lab conditions. To identify cues that stimulate germination, we explored whether host factors could induce high germination rates. In this study, we demonstrate that C. pseudonaviculata spores achieve high germination rates when they are placed on detached leaves of boxwood and other known hosts, compared to potato dextrose agar and glass coverslips. We also demonstrate that germination is induced by volatiles from detached leaves of boxwood, as well as the nonhost Berberis thunbergii. When C. pseudonaviculata spores were exposed to volatiles from boxwood leaves in the presence of ethylene scrubber packs that contained potassium permanganate, the stimulatory effect on spore germination was reduced. However, ethylene, a regulator of leaf senescence, did not stimulate germination of C. pseudonaviculata spores. This suggests that the pathogen may have evolved to recognize one or more host volatiles, other than ethylene to induce germination, thus limiting its growth until it senses the presence of a host plant.
{"title":"The Effect of Boxwood Leaf Volatiles on Conidial Germination of <i>Calonectria pseudonaviculata</i>, the Causal Agent of Boxwood Blight.","authors":"Mana Ohkura, Bryan R Beck, Carolyn F Scagel, Jerry E Weiland","doi":"10.1094/PHYTO-12-23-0507-R","DOIUrl":"10.1094/PHYTO-12-23-0507-R","url":null,"abstract":"<p><p>The fungal pathogen <i>Calonectria pseudonaviculata</i> causes boxwood blight and is a significant threat to the boxwood industry, as well as historic boxwood gardens. The pathogen produces conidia in sticky masses that are splash dispersed, which germinate and infect through stomata on the leaves or stems, causing leaf spots and stem lesions. Despite its ability to cause severe infections on boxwood plants, the pathogen often has a low germination rate on artificial media under lab conditions. To identify cues that stimulate germination, we explored whether host factors could induce high germination rates. In this study, we demonstrate that <i>C. pseudonaviculata</i> spores achieve high germination rates when they are placed on detached leaves of boxwood and other known hosts, compared to potato dextrose agar and glass coverslips. We also demonstrate that germination is induced by volatiles from detached leaves of boxwood, as well as the nonhost <i>Berberis thunbergii</i>. When <i>C. pseudonaviculata</i> spores were exposed to volatiles from boxwood leaves in the presence of ethylene scrubber packs that contained potassium permanganate, the stimulatory effect on spore germination was reduced. However, ethylene, a regulator of leaf senescence, did not stimulate germination of <i>C. pseudonaviculata</i> spores. This suggests that the pathogen may have evolved to recognize one or more host volatiles, other than ethylene to induce germination, thus limiting its growth until it senses the presence of a host plant.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140306619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-07-11DOI: 10.1094/PHYTO-03-24-0106-SC
Lanfei Zhao, Amy Bernardo, Fanmei Kong, Wei Zhao, Yanhong Dong, Hyeonju Lee, Harold N Trick, Jessica Rupp Noller, Guihua Bai
Fusarium head blight (FHB), mainly incited by Fusarium graminearum, has caused great losses in grain yield and quality of wheat globally. Fhb7, a major gene from 7E chromosome of Thinopyrum ponticum, confers broad resistance to multiple Fusarium species in wheat and has recently been cloned and identified as encoding a glutathione S-transferase (GST). However, some recent reports raised doubt about whether GST is the causal gene of Fhb7. To resolve the discrepancy and validate the gene function of GST in wheat, we phenotyped Fhb7 near-isogenic lines (Jimai22-Fhb7 versus Jimai22) and GST overexpressed lines for FHB resistance. Jimai22-Fhb7 showed significantly higher FHB resistance with a lower percentage of symptomatic spikelets, Fusarium-damaged kernels, and deoxynivalenol content than susceptible Jimai22 in three experiments. All the positive GST transgenic lines driven by either the maize ubiquitin promoter or its native promoter with high gene expression in the wheat cultivar 'Fielder' showed high FHB resistance. Only one maize ubiquitin promoter-driven transgenic line showed low GST expression and similar susceptibility to Fielder, suggesting that high GST expression confers Fhb7 resistance to FHB. Knockout of GST in the Jimai22-Fhb7 line using CRISPR-Cas9-based gene editing showed significantly higher FHB susceptibility compared with the nonedited control plants. Therefore, we confirmed GST as the causal gene of Fhb7 for FHB resistance. Considering its major effect on FHB resistance, pyramiding Fhb7 with other quantitative trait loci has a great potential to create highly FHB-resistant wheat cultivars.
{"title":"A Glutathione S-Transferase from <i>Thinopyrum ponticum</i> Confers <i>Fhb7</i> Resistance to Fusarium Head Blight in Wheat.","authors":"Lanfei Zhao, Amy Bernardo, Fanmei Kong, Wei Zhao, Yanhong Dong, Hyeonju Lee, Harold N Trick, Jessica Rupp Noller, Guihua Bai","doi":"10.1094/PHYTO-03-24-0106-SC","DOIUrl":"10.1094/PHYTO-03-24-0106-SC","url":null,"abstract":"<p><p>Fusarium head blight (FHB), mainly incited by <i>Fusarium graminearum</i>, has caused great losses in grain yield and quality of wheat globally. <i>Fhb7</i>, a major gene from 7E chromosome of <i>Thinopyrum ponticum</i>, confers broad resistance to multiple <i>Fusarium</i> species in wheat and has recently been cloned and identified as encoding a glutathione S-transferase (<i>GST</i>). However, some recent reports raised doubt about whether <i>GST</i> is the causal gene of <i>Fhb7</i>. To resolve the discrepancy and validate the gene function of <i>GST</i> in wheat, we phenotyped <i>Fhb7</i> near-isogenic lines (Jimai22-<i>Fhb7</i> versus Jimai22) and <i>GST</i> overexpressed lines for FHB resistance. Jimai22-<i>Fhb7</i> showed significantly higher FHB resistance with a lower percentage of symptomatic spikelets, <i>Fusarium</i>-damaged kernels, and deoxynivalenol content than susceptible Jimai22 in three experiments. All the positive <i>GST</i> transgenic lines driven by either the maize ubiquitin promoter or its native promoter with high gene expression in the wheat cultivar 'Fielder' showed high FHB resistance. Only one maize ubiquitin promoter-driven transgenic line showed low <i>GST</i> expression and similar susceptibility to Fielder, suggesting that high <i>GST</i> expression confers <i>Fhb7</i> resistance to FHB. Knockout of <i>GST</i> in the Jimai22-<i>Fhb7</i> line using CRISPR-Cas9-based gene editing showed significantly higher FHB susceptibility compared with the nonedited control plants. Therefore, we confirmed <i>GST</i> as the causal gene of <i>Fhb7</i> for FHB resistance. Considering its major effect on FHB resistance, pyramiding <i>Fhb7</i> with other quantitative trait loci has a great potential to create highly FHB-resistant wheat cultivars.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140859955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-07-10DOI: 10.1094/PHYTO-01-24-0025-R
Jaimie R Kenney, Tessa Shates, Marco Gebiola, Kerry E Mauck
The unculturable bacterium 'Candidatus Liberibacter solanacearum' (CLso) is responsible for a growing number of emerging crop diseases. However, we know little about the diversity and ecology of CLso and its psyllid vectors outside of agricultural systems, which limits our ability to manage crop disease and understand the impacts this pathogen may have on wild plants in natural ecosystems. In North America, CLso is transmitted to crops by the native potato psyllid (Bactericera cockerelli). However, the geographic and host plant range of the potato psyllid and CLso beyond the borders of agriculture are not well understood. A recent study of historic herbarium specimens revealed that a unique haplotype of CLso was present infecting populations of the native perennial Solanum umbelliferum in California decades before CLso was first detected in crops. We hypothesized that this haplotype and other potentially novel CLso variants are still present in S. umbelliferum populations. To test this, we surveyed populations of S. umbelliferum in Southern California for CLso and potato psyllid vectors. We found multiple haplotypes of CLso and the potato psyllid associated with these populations, with none of these genetic variants having been previously reported in California crops. These results suggest that CLso and its psyllid vectors are much more widespread and diverse in North American natural plant communities than suggested by data collected solely from crops and weeds in agricultural fields. Further characterization of these apparently asymptomatic haplotypes will facilitate comparison with disease-causing variants and provide insights into the continued emergence and spread of CLso.
{"title":"Hiding in Plain Sight: A Widespread Native Perennial Harbors Diverse Haplotypes of '<i>Candidatus</i> Liberibacter solanacearum' and Its Potato Psyllid Vector.","authors":"Jaimie R Kenney, Tessa Shates, Marco Gebiola, Kerry E Mauck","doi":"10.1094/PHYTO-01-24-0025-R","DOIUrl":"10.1094/PHYTO-01-24-0025-R","url":null,"abstract":"<p><p>The unculturable bacterium '<i>Candidatus</i> Liberibacter solanacearum' (CLso) is responsible for a growing number of emerging crop diseases. However, we know little about the diversity and ecology of CLso and its psyllid vectors outside of agricultural systems, which limits our ability to manage crop disease and understand the impacts this pathogen may have on wild plants in natural ecosystems. In North America, CLso is transmitted to crops by the native potato psyllid (<i>Bactericera cockerelli</i>). However, the geographic and host plant range of the potato psyllid and CLso beyond the borders of agriculture are not well understood. A recent study of historic herbarium specimens revealed that a unique haplotype of CLso was present infecting populations of the native perennial <i>Solanum umbelliferum</i> in California decades before CLso was first detected in crops. We hypothesized that this haplotype and other potentially novel CLso variants are still present in <i>S. umbelliferum</i> populations. To test this, we surveyed populations of <i>S. umbelliferum</i> in Southern California for CLso and potato psyllid vectors. We found multiple haplotypes of CLso and the potato psyllid associated with these populations, with none of these genetic variants having been previously reported in California crops. These results suggest that CLso and its psyllid vectors are much more widespread and diverse in North American natural plant communities than suggested by data collected solely from crops and weeds in agricultural fields. Further characterization of these apparently asymptomatic haplotypes will facilitate comparison with disease-causing variants and provide insights into the continued emergence and spread of CLso.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140870942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-06-10DOI: 10.1094/PHYTO-12-23-0480-R
Armelle Marais, Pascal Gentit, Yoann Brans, Jean Philippe Renvoisé, Chantal Faure, Anne Saison, Pascaline Cousseau, Julie Castaing, Fabien Chambon, Angélique Pion, Grégory Calado, Marie Lefebvre, Soraya Garnier, François Latour, Kévin Bresson, Nathalie Grasseau, Thierry Candresse
There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.
{"title":"Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops.","authors":"Armelle Marais, Pascal Gentit, Yoann Brans, Jean Philippe Renvoisé, Chantal Faure, Anne Saison, Pascaline Cousseau, Julie Castaing, Fabien Chambon, Angélique Pion, Grégory Calado, Marie Lefebvre, Soraya Garnier, François Latour, Kévin Bresson, Nathalie Grasseau, Thierry Candresse","doi":"10.1094/PHYTO-12-23-0480-R","DOIUrl":"10.1094/PHYTO-12-23-0480-R","url":null,"abstract":"<p><p>There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139913278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Early detection of rice blast disease is pivotal to ensure rice yield. We collected in situ images of rice blast and constructed a rice blast dataset based on variations in lesion shape, size, and color. Given that rice blast lesions are small and typically exhibit round, oval, and fusiform shapes, we proposed a small object detection model named GCPDFFNet (global context-based parallel differentiation feature fusion network) for rice blast recognition. The GCPDFFNet model has three global context feature extraction modules and two parallel differentiation feature fusion modules. The global context modules are employed to focus on the lesion areas; the parallel differentiation feature fusion modules are used to enhance the recognition effect of small-sized lesions. In addition, we proposed the SCYLLA normalized Wasserstein distance loss function, specifically designed to accelerate model convergence and improve the detection accuracy of rice blast disease. Comparative experiments were conducted on the rice blast dataset to evaluate the performance of the model. The proposed GCPDFFNet model outperformed the baseline network CenterNet, with a significant increase in mean average precision from 83.6 to 95.4% on the rice blast test set while maintaining a satisfactory frames per second drop from 147.9 to 122.1. Our results suggest that the GCPDFFNet model can accurately detect in situ rice blast disease while ensuring the inference speed meets the real-time requirements.
{"title":"GCPDFFNet: Small Object Detection for Rice Blast Recognition.","authors":"Dejin Xie, Wei Ye, Yining Pan, Jiaoyu Wang, Haiping Qiu, Hongkai Wang, Zhaoxing Li, Tianhao Chen","doi":"10.1094/PHYTO-09-23-0326-R","DOIUrl":"10.1094/PHYTO-09-23-0326-R","url":null,"abstract":"<p><p>Early detection of rice blast disease is pivotal to ensure rice yield. We collected in situ images of rice blast and constructed a rice blast dataset based on variations in lesion shape, size, and color. Given that rice blast lesions are small and typically exhibit round, oval, and fusiform shapes, we proposed a small object detection model named GCPDFFNet (global context-based parallel differentiation feature fusion network) for rice blast recognition. The GCPDFFNet model has three global context feature extraction modules and two parallel differentiation feature fusion modules. The global context modules are employed to focus on the lesion areas; the parallel differentiation feature fusion modules are used to enhance the recognition effect of small-sized lesions. In addition, we proposed the SCYLLA normalized Wasserstein distance loss function, specifically designed to accelerate model convergence and improve the detection accuracy of rice blast disease. Comparative experiments were conducted on the rice blast dataset to evaluate the performance of the model. The proposed GCPDFFNet model outperformed the baseline network CenterNet, with a significant increase in mean average precision from 83.6 to 95.4% on the rice blast test set while maintaining a satisfactory frames per second drop from 147.9 to 122.1. Our results suggest that the GCPDFFNet model can accurately detect in situ rice blast disease while ensuring the inference speed meets the real-time requirements.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}