Pub Date : 2024-04-15DOI: 10.1094/phytofr-03-24-0021-a
Fu-Hua Zhao, Yue Li, Hong-Yue Qi, Hengguang Zhu, Ran Li, Jiemin Chen, X. Dai, Dan Wang, Dongfei Han, Xiaojun Zhang
Bacillus mojavensis KRS009 was identified as antagonistic strain with strong inhibitory effect to various phytopathogenic fungi. To provide a further insight into its biocontrol mechanisms and ability to improve plant salt tolerance, the high-quality complete genome of KRS009 was sequenced and assembled using PacBio-HiFiReads. KRS009 genome consists of one circular chromosome as 4,089,687 bp with 43.5% GC content. 4,062 open reading frames, of which 3,920 protein-coding genes, 86 transfer RNA, 10 ribosomal RNA, and 26 small RNA were identified in this genome. Among them, genes related to compatible solutes, including treC, galU, proX, and proW, are involved in the synthesis of trehalose, proline, and betaine metabolism, play important role in relieving osmotic stress. In addition, the KRS009 genome contains genes associated with high salinity tolerance, including those responsible for Na+/H+ antiporters, K+ transporters TrkH thiamin phosphate synthase, K+-sensing histidine kinase, aryl-phospho-beta-D-glucosidase, flavoprotein CzcO associated with the cation diffusion facilitator CzcD and chaperonin GroEL. Together, the high-quality genome resource of strain KRS009 would provide molecular basis for further research on its biocontrol and plant salt tolerance mechanisms.
{"title":"Genome Sequence Resource of Bacillus mojavensis KRS009, a Rhizospheric Microorganism with Biocontrol Potential","authors":"Fu-Hua Zhao, Yue Li, Hong-Yue Qi, Hengguang Zhu, Ran Li, Jiemin Chen, X. Dai, Dan Wang, Dongfei Han, Xiaojun Zhang","doi":"10.1094/phytofr-03-24-0021-a","DOIUrl":"https://doi.org/10.1094/phytofr-03-24-0021-a","url":null,"abstract":"Bacillus mojavensis KRS009 was identified as antagonistic strain with strong inhibitory effect to various phytopathogenic fungi. To provide a further insight into its biocontrol mechanisms and ability to improve plant salt tolerance, the high-quality complete genome of KRS009 was sequenced and assembled using PacBio-HiFiReads. KRS009 genome consists of one circular chromosome as 4,089,687 bp with 43.5% GC content. 4,062 open reading frames, of which 3,920 protein-coding genes, 86 transfer RNA, 10 ribosomal RNA, and 26 small RNA were identified in this genome. Among them, genes related to compatible solutes, including treC, galU, proX, and proW, are involved in the synthesis of trehalose, proline, and betaine metabolism, play important role in relieving osmotic stress. In addition, the KRS009 genome contains genes associated with high salinity tolerance, including those responsible for Na+/H+ antiporters, K+ transporters TrkH thiamin phosphate synthase, K+-sensing histidine kinase, aryl-phospho-beta-D-glucosidase, flavoprotein CzcO associated with the cation diffusion facilitator CzcD and chaperonin GroEL. Together, the high-quality genome resource of strain KRS009 would provide molecular basis for further research on its biocontrol and plant salt tolerance mechanisms.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"333 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140703653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1094/phytofr-09-23-0121-r
Mariama T. Brown, Sungchan Oh, Katy M. Rainey, Darcy. E. P. Telenko
Sudden death syndrome (SDS) of soybean is caused by a soil-borne pathogen, Fusarium virguliforme. Prior to visible foliar symptoms, a destructive technique is usually carried out to diagnose root infection. The use of hyperspectral sensors for pre-symptomatic and non-destructive plant disease diagnosis has been on the rise. This study was designed to relate leaf spectral reflectance to F. virguliforme root infection in the absence of foliar symptoms. Soybean plants were grown under controlled greenhouse conditions. The plants’ spectral reflectance was measured weekly beginning at 21 days after transplanting (DAT) up until 42 DAT using a swing hyperspectral imaging system that is fixed on a gantry. Destructive root sampling confirmed F. virguliforme root infection using Real-time PCR. The most relevant wavelengths for discrimination were selected using the ReliefF algorithm. Three machine learning models [Partial least squares discriminant analysis (PLS-DA), support vector machine, and random forest] were evaluated for classification accuracy using the selected wavelengths. Relevant wavelengths for differentiating between the healthy and F. virguliforme infected plants were found in the visible and red-edge region from 500 to 750 nm, and the shortwave infrared region from 1400 to 2350 nm. In the absence of visible foliar symptoms, classification results showed over 79% mean F1-scores for all models. PLS-DA was able to differentiate healthy and F. virguliforme infected plants with a mean F1-score of 83.1 to 85.3% and a kappa statistic of 0.43 to 0.54. This work supports the use of hyperspectral remote sensing for early pre-symptomatic disease diagnosis under controlled environment.
{"title":"Pre-symptomatic leaf reflectance of Fusarium virguliforme infected soybean plants in greenhouse conditions","authors":"Mariama T. Brown, Sungchan Oh, Katy M. Rainey, Darcy. E. P. Telenko","doi":"10.1094/phytofr-09-23-0121-r","DOIUrl":"https://doi.org/10.1094/phytofr-09-23-0121-r","url":null,"abstract":"Sudden death syndrome (SDS) of soybean is caused by a soil-borne pathogen, Fusarium virguliforme. Prior to visible foliar symptoms, a destructive technique is usually carried out to diagnose root infection. The use of hyperspectral sensors for pre-symptomatic and non-destructive plant disease diagnosis has been on the rise. This study was designed to relate leaf spectral reflectance to F. virguliforme root infection in the absence of foliar symptoms. Soybean plants were grown under controlled greenhouse conditions. The plants’ spectral reflectance was measured weekly beginning at 21 days after transplanting (DAT) up until 42 DAT using a swing hyperspectral imaging system that is fixed on a gantry. Destructive root sampling confirmed F. virguliforme root infection using Real-time PCR. The most relevant wavelengths for discrimination were selected using the ReliefF algorithm. Three machine learning models [Partial least squares discriminant analysis (PLS-DA), support vector machine, and random forest] were evaluated for classification accuracy using the selected wavelengths. Relevant wavelengths for differentiating between the healthy and F. virguliforme infected plants were found in the visible and red-edge region from 500 to 750 nm, and the shortwave infrared region from 1400 to 2350 nm. In the absence of visible foliar symptoms, classification results showed over 79% mean F1-scores for all models. PLS-DA was able to differentiate healthy and F. virguliforme infected plants with a mean F1-score of 83.1 to 85.3% and a kappa statistic of 0.43 to 0.54. This work supports the use of hyperspectral remote sensing for early pre-symptomatic disease diagnosis under controlled environment.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"1480 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140773948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-13DOI: 10.1094/phytofr-02-24-0012-r
D. Weller, Johan A Van Pelt, L. Thomashow, D. Mavrodi, O. Mavrodi, C. Pieterse, P. A. H. M. Bakker
Arabidopsis thaliana accession Col-0 seedlings were transferred into an autoclaved potting soil/sand mixture amended with either 10 or 20% (weight/weight) soil from fields in Washington State USA that are suppressive to take-all or Rhizoctonia root rot of wheat. Three weeks after transplanting, these plants had population sizes of 2,4-diacetylphloroglucinol (DAPG)- or phenazine-1-carboxylic acid (PCA)-producing pseudomonads of greater than 5 x 105 colony forming units per gram fresh weight of root with rhizosphere soil. When the plants were challenge-inoculated with Pseudomonas syringae pv. tomato, both soils displayed induced systemic resistance in the leaves against bacterial speck to a level similar to that induced by Pseudomonas simiae WCS417r, P. fluorescens Q2-87 (DAPG+), P. brassicacearum Q8r1-96 and L5.1-96 (both DAPG+), and P. synxantha 2-79 (PCA+). Pasteurization of the soils before adding them into the soil/sand mixture eliminated DAPG- and PCA-producing pseudomonads from the A. thaliana rhizosphere and significantly reduced induced systemic resistance activity. However, populations of total culturable heterotrophic aerobic bacteria were similar in the rhizosphere of plants grown in soil/sand mixes amended with untreated or pasteurized suppressive soils. This is the first report of induction of systemic resistance in A. thaliana by take-all and Rhizoctonia suppressive soils and the ability of PCA-producing P. synxantha 2-79 to induce resistance.
{"title":"Disease-suppressive soils induce systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato","authors":"D. Weller, Johan A Van Pelt, L. Thomashow, D. Mavrodi, O. Mavrodi, C. Pieterse, P. A. H. M. Bakker","doi":"10.1094/phytofr-02-24-0012-r","DOIUrl":"https://doi.org/10.1094/phytofr-02-24-0012-r","url":null,"abstract":"Arabidopsis thaliana accession Col-0 seedlings were transferred into an autoclaved potting soil/sand mixture amended with either 10 or 20% (weight/weight) soil from fields in Washington State USA that are suppressive to take-all or Rhizoctonia root rot of wheat. Three weeks after transplanting, these plants had population sizes of 2,4-diacetylphloroglucinol (DAPG)- or phenazine-1-carboxylic acid (PCA)-producing pseudomonads of greater than 5 x 105 colony forming units per gram fresh weight of root with rhizosphere soil. When the plants were challenge-inoculated with Pseudomonas syringae pv. tomato, both soils displayed induced systemic resistance in the leaves against bacterial speck to a level similar to that induced by Pseudomonas simiae WCS417r, P. fluorescens Q2-87 (DAPG+), P. brassicacearum Q8r1-96 and L5.1-96 (both DAPG+), and P. synxantha 2-79 (PCA+). Pasteurization of the soils before adding them into the soil/sand mixture eliminated DAPG- and PCA-producing pseudomonads from the A. thaliana rhizosphere and significantly reduced induced systemic resistance activity. However, populations of total culturable heterotrophic aerobic bacteria were similar in the rhizosphere of plants grown in soil/sand mixes amended with untreated or pasteurized suppressive soils. This is the first report of induction of systemic resistance in A. thaliana by take-all and Rhizoctonia suppressive soils and the ability of PCA-producing P. synxantha 2-79 to induce resistance.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140245667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-04DOI: 10.1094/phytofr-01-24-0004-a
María Pilar Velasco-Amo, Luis F. Arias-Giraldo, M. Román-Écija, A. Giampetruzzi, M. Saponari, Blanca B. Landa
Xylella fastidiosa (Xf) is a vascular phytopathogenic bacterium native to the Americas, known for causing severe diseases and significant economic losses in important crops. In Europe, Xf is considered a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys to search for Xf across Europe revealed the presence of three Xf subspecies (fastidiosa, multiplex and pauca) in different outbreaks occurring in France, Spain, and Portugal. Xf subspecies sandyi and morus have not been associated to epidemic outbreaks in Europe; however, subspecies sandyi has been detected in intercepted plants imported from Costa Rica and Honduras. By combining data from the Oxford Nanopore Technologies and Illumina sequencing platforms, we obtained complete genomes for Xf strains CO33 and CFBP8478. Both strains belong to the subspecies sandyi and were isolated from coffee plants intercepted in Europe that were imported from Costa Rica. These two genome resources increase the scarce number of Xf genomes available belonging to the subspecies sandyi which is crucial for comparative genomic analysis and population studies of this important plant pathogenic bacterium.
{"title":"Complete circularized genome resources for Xylella fastidiosa subsp. sandyi strains CO33 and CFBP8478","authors":"María Pilar Velasco-Amo, Luis F. Arias-Giraldo, M. Román-Écija, A. Giampetruzzi, M. Saponari, Blanca B. Landa","doi":"10.1094/phytofr-01-24-0004-a","DOIUrl":"https://doi.org/10.1094/phytofr-01-24-0004-a","url":null,"abstract":"Xylella fastidiosa (Xf) is a vascular phytopathogenic bacterium native to the Americas, known for causing severe diseases and significant economic losses in important crops. In Europe, Xf is considered a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys to search for Xf across Europe revealed the presence of three Xf subspecies (fastidiosa, multiplex and pauca) in different outbreaks occurring in France, Spain, and Portugal. Xf subspecies sandyi and morus have not been associated to epidemic outbreaks in Europe; however, subspecies sandyi has been detected in intercepted plants imported from Costa Rica and Honduras. By combining data from the Oxford Nanopore Technologies and Illumina sequencing platforms, we obtained complete genomes for Xf strains CO33 and CFBP8478. Both strains belong to the subspecies sandyi and were isolated from coffee plants intercepted in Europe that were imported from Costa Rica. These two genome resources increase the scarce number of Xf genomes available belonging to the subspecies sandyi which is crucial for comparative genomic analysis and population studies of this important plant pathogenic bacterium.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"22 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140080684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-01DOI: 10.1094/phytofr-11-23-0143-sc
Timothy O. Jobe, Michael Urner, Mauricio Ulloa, K. Broders, R. Hutmacher, Margaret L Ellis
Many Fusarium oxysporum formae speciales produce small, infection-dependent effector proteins called ‘secreted in xylem’ (SIX) proteins. These proteins are secreted into the xylem of a plant during the infection process and are thought to promote virulence. In this study, a collection of Fusarium oxysporum isolates composed primarily of different races of Fusarium oxysporum f. sp. vasinfectum (FOV), was screened for the presence of fourteen SIX effector genes (SIX1-SIX14). Our results showed that some of the most virulent FOV races, FOV4 and FOV7, share a common SIX effector – SIX9. This effector is largely absent in other races of FOV in North America making SIX9 a potential target for rapid detection of these highly virulent FOV strains and enabling race specific FOV quantification in infected host plants.
许多恶孢镰刀菌特异株会产生依赖于感染的小型效应蛋白，称为 "木质部分泌"（SIX）蛋白。这些蛋白在感染过程中分泌到植物木质部，被认为能增强毒力。在这项研究中，我们对主要由 Fusarium oxysporum f. sp. vasinfectum（FOV）不同品系组成的 Fusarium oxysporum 分离物进行了筛选，以检测是否存在 14 个 SIX 效应基因（SIX1-SIX14）。我们的研究结果表明，FOV4 和 FOV7 这两个毒性最强的 FOV 株系共享一个共同的 SIX 效应子--SIX9。这种效应子在北美的其他 FOV 种族中基本不存在，因此 SIX9 成为快速检测这些高致病性 FOV 菌株的潜在目标，并能对受感染寄主植物中的特定 FOV 种族进行定量。
{"title":"Secreted in xylem (SIX) gene SIX9 is highly conserved in Fusarium oxysporum f. sp. vasinfectum race 4 isolates from cotton in the United States","authors":"Timothy O. Jobe, Michael Urner, Mauricio Ulloa, K. Broders, R. Hutmacher, Margaret L Ellis","doi":"10.1094/phytofr-11-23-0143-sc","DOIUrl":"https://doi.org/10.1094/phytofr-11-23-0143-sc","url":null,"abstract":"Many Fusarium oxysporum formae speciales produce small, infection-dependent effector proteins called ‘secreted in xylem’ (SIX) proteins. These proteins are secreted into the xylem of a plant during the infection process and are thought to promote virulence. In this study, a collection of Fusarium oxysporum isolates composed primarily of different races of Fusarium oxysporum f. sp. vasinfectum (FOV), was screened for the presence of fourteen SIX effector genes (SIX1-SIX14). Our results showed that some of the most virulent FOV races, FOV4 and FOV7, share a common SIX effector – SIX9. This effector is largely absent in other races of FOV in North America making SIX9 a potential target for rapid detection of these highly virulent FOV strains and enabling race specific FOV quantification in infected host plants.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"84 19","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140086637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-01DOI: 10.1094/phytofr-02-24-0005-fi
Walter F. Mahaffee, L. Thiessen, Kevin M. King, R. Choudhury
{"title":"Detection and Monitoring of Plant Pathogens and Pests","authors":"Walter F. Mahaffee, L. Thiessen, Kevin M. King, R. Choudhury","doi":"10.1094/phytofr-02-24-0005-fi","DOIUrl":"https://doi.org/10.1094/phytofr-02-24-0005-fi","url":null,"abstract":"","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"86 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140282413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-08DOI: 10.1094/phytofr-01-24-0001-r
Hannah M. Rivedal, Todd N. Temple, Robert J. Starchvick, Emily Braithwaite, Sarah R. Lowder, Seth J. Dorman, L. A. Núñez Rodríguez, A. Peetz, Inga A. Zasada
Oregon’s grass seed industry specializes in the production of forage grasses, including annual ryegrass (Lolium multiflorum) and orchardgrass (Dactylis glomerata). These species are hosts of seed gall nematodes (SGN): Anguina funesta and Anguina sp. SGN cause yield-limiting seed galls and can also vector toxic Rathayibacter bacteria. Trade partners have strict phytosanitary regulations leading to rejection of seed lots infested with SGN. Current best practices for SGN detection focus on post-harvest seed evaluation. Methods to evaluate fields before harvest could improve risk management decisions. In this study, we evaluated timing, collection, and detection methods to generate new recommendations for SGN detection throughout the growing season. Fields of annual ryegrass (21) and orchardgrass (7) were sampled in the 2022 and 2023 growing seasons at tillering (March), flowering (May), harvest (July), and germination (November). At each time point, tillers, seed heads or soil samples were collected. Nematodes were extracted from soil, tiller, and seed head samples using traditional nematology methods. Alternatively, SGN-specific real-time and conventional PCR protocols were evaluated on DNA extracted from tillers or seed heads. Direct enumeration of SGN from tillers with traditional nematology methods resulted in positive detections in 11-19% of fields depending on sample time and year as opposed to 33-44% of fields when using molecular methods. SGN were detected in 40% of fields using both methods when evaluating seed head samples. This study indicates the utility of incorporating molecular methods for risk evaluations of SGN and provides recommendations for the accurate detection of SGN throughout the growing season.
{"title":"Comparison of molecular and morphological identification methods for Anguina seed gall nematodes in Oregon grasses grown for seed","authors":"Hannah M. Rivedal, Todd N. Temple, Robert J. Starchvick, Emily Braithwaite, Sarah R. Lowder, Seth J. Dorman, L. A. Núñez Rodríguez, A. Peetz, Inga A. Zasada","doi":"10.1094/phytofr-01-24-0001-r","DOIUrl":"https://doi.org/10.1094/phytofr-01-24-0001-r","url":null,"abstract":"Oregon’s grass seed industry specializes in the production of forage grasses, including annual ryegrass (Lolium multiflorum) and orchardgrass (Dactylis glomerata). These species are hosts of seed gall nematodes (SGN): Anguina funesta and Anguina sp. SGN cause yield-limiting seed galls and can also vector toxic Rathayibacter bacteria. Trade partners have strict phytosanitary regulations leading to rejection of seed lots infested with SGN. Current best practices for SGN detection focus on post-harvest seed evaluation. Methods to evaluate fields before harvest could improve risk management decisions. In this study, we evaluated timing, collection, and detection methods to generate new recommendations for SGN detection throughout the growing season. Fields of annual ryegrass (21) and orchardgrass (7) were sampled in the 2022 and 2023 growing seasons at tillering (March), flowering (May), harvest (July), and germination (November). At each time point, tillers, seed heads or soil samples were collected. Nematodes were extracted from soil, tiller, and seed head samples using traditional nematology methods. Alternatively, SGN-specific real-time and conventional PCR protocols were evaluated on DNA extracted from tillers or seed heads. Direct enumeration of SGN from tillers with traditional nematology methods resulted in positive detections in 11-19% of fields depending on sample time and year as opposed to 33-44% of fields when using molecular methods. SGN were detected in 40% of fields using both methods when evaluating seed head samples. This study indicates the utility of incorporating molecular methods for risk evaluations of SGN and provides recommendations for the accurate detection of SGN throughout the growing season.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139852420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-08DOI: 10.1094/phytofr-01-24-0001-r
Hannah M. Rivedal, Todd N. Temple, Robert J. Starchvick, Emily Braithwaite, Sarah R. Lowder, Seth J. Dorman, L. A. Núñez Rodríguez, A. Peetz, Inga A. Zasada
Oregon’s grass seed industry specializes in the production of forage grasses, including annual ryegrass (Lolium multiflorum) and orchardgrass (Dactylis glomerata). These species are hosts of seed gall nematodes (SGN): Anguina funesta and Anguina sp. SGN cause yield-limiting seed galls and can also vector toxic Rathayibacter bacteria. Trade partners have strict phytosanitary regulations leading to rejection of seed lots infested with SGN. Current best practices for SGN detection focus on post-harvest seed evaluation. Methods to evaluate fields before harvest could improve risk management decisions. In this study, we evaluated timing, collection, and detection methods to generate new recommendations for SGN detection throughout the growing season. Fields of annual ryegrass (21) and orchardgrass (7) were sampled in the 2022 and 2023 growing seasons at tillering (March), flowering (May), harvest (July), and germination (November). At each time point, tillers, seed heads or soil samples were collected. Nematodes were extracted from soil, tiller, and seed head samples using traditional nematology methods. Alternatively, SGN-specific real-time and conventional PCR protocols were evaluated on DNA extracted from tillers or seed heads. Direct enumeration of SGN from tillers with traditional nematology methods resulted in positive detections in 11-19% of fields depending on sample time and year as opposed to 33-44% of fields when using molecular methods. SGN were detected in 40% of fields using both methods when evaluating seed head samples. This study indicates the utility of incorporating molecular methods for risk evaluations of SGN and provides recommendations for the accurate detection of SGN throughout the growing season.
{"title":"Comparison of molecular and morphological identification methods for Anguina seed gall nematodes in Oregon grasses grown for seed","authors":"Hannah M. Rivedal, Todd N. Temple, Robert J. Starchvick, Emily Braithwaite, Sarah R. Lowder, Seth J. Dorman, L. A. Núñez Rodríguez, A. Peetz, Inga A. Zasada","doi":"10.1094/phytofr-01-24-0001-r","DOIUrl":"https://doi.org/10.1094/phytofr-01-24-0001-r","url":null,"abstract":"Oregon’s grass seed industry specializes in the production of forage grasses, including annual ryegrass (Lolium multiflorum) and orchardgrass (Dactylis glomerata). These species are hosts of seed gall nematodes (SGN): Anguina funesta and Anguina sp. SGN cause yield-limiting seed galls and can also vector toxic Rathayibacter bacteria. Trade partners have strict phytosanitary regulations leading to rejection of seed lots infested with SGN. Current best practices for SGN detection focus on post-harvest seed evaluation. Methods to evaluate fields before harvest could improve risk management decisions. In this study, we evaluated timing, collection, and detection methods to generate new recommendations for SGN detection throughout the growing season. Fields of annual ryegrass (21) and orchardgrass (7) were sampled in the 2022 and 2023 growing seasons at tillering (March), flowering (May), harvest (July), and germination (November). At each time point, tillers, seed heads or soil samples were collected. Nematodes were extracted from soil, tiller, and seed head samples using traditional nematology methods. Alternatively, SGN-specific real-time and conventional PCR protocols were evaluated on DNA extracted from tillers or seed heads. Direct enumeration of SGN from tillers with traditional nematology methods resulted in positive detections in 11-19% of fields depending on sample time and year as opposed to 33-44% of fields when using molecular methods. SGN were detected in 40% of fields using both methods when evaluating seed head samples. This study indicates the utility of incorporating molecular methods for risk evaluations of SGN and provides recommendations for the accurate detection of SGN throughout the growing season.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":" 22","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139792649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-01DOI: 10.1094/phytofr-10-23-0135-a
Maricel Gonzales, Brian L. Abernathy, Robert Kemerait, David Bertioli, Marin Brewer, Soraya Leal-Bertioli
Nothopassalora personata, the causal agent of late leaf spot, is an economically important fungus that poses a significant threat to peanut production worldwide. Currently, studies on N. personata are focused on epidemiology, host resistance, early environmental detection, and molecular studies based on a limited number of genes for classification. A high-quality whole genome sequence can be a valuable tool for studying complex species and identifying molecular mechanisms in pathogenicity and adaptation. This study reports a high-quality, chromosome-scale genome assembly for N. personata with a total length of 54.6 Mb, an N50 of 2.54 Mb, a longest contig length of 4.47 Mb and a BUSCO genome completeness score of 99.5% with mostly single copy genes. Genome annotation revealed 11,295 protein-encoding genes and 12,121 transcripts in which 411 of the 995 predicted proteins were putative effectors. Genome comparison with the closely related fungi Dothistroma septosporum NZE10 and Fulvia fulva (syn. Passalora fulva, Cladosporium fulvum) isolate Race 5 revealed 13 chromosomes. This genome sequence resource can be used as a reference for aligning sequences of multiple isolates to provide relevant information on the diversity and population genetic structure of N. personata to further inform peanut resistance breeding programs and devise the best disease management strategies.
{"title":"Chromosome-scale genome sequence of Nothopassalora personata (syn. Cercosporidium personatum), a devastating fungal pathogen of peanut","authors":"Maricel Gonzales, Brian L. Abernathy, Robert Kemerait, David Bertioli, Marin Brewer, Soraya Leal-Bertioli","doi":"10.1094/phytofr-10-23-0135-a","DOIUrl":"https://doi.org/10.1094/phytofr-10-23-0135-a","url":null,"abstract":"Nothopassalora personata, the causal agent of late leaf spot, is an economically important fungus that poses a significant threat to peanut production worldwide. Currently, studies on N. personata are focused on epidemiology, host resistance, early environmental detection, and molecular studies based on a limited number of genes for classification. A high-quality whole genome sequence can be a valuable tool for studying complex species and identifying molecular mechanisms in pathogenicity and adaptation. This study reports a high-quality, chromosome-scale genome assembly for N. personata with a total length of 54.6 Mb, an N50 of 2.54 Mb, a longest contig length of 4.47 Mb and a BUSCO genome completeness score of 99.5% with mostly single copy genes. Genome annotation revealed 11,295 protein-encoding genes and 12,121 transcripts in which 411 of the 995 predicted proteins were putative effectors. Genome comparison with the closely related fungi Dothistroma septosporum NZE10 and Fulvia fulva (syn. Passalora fulva, Cladosporium fulvum) isolate Race 5 revealed 13 chromosomes. This genome sequence resource can be used as a reference for aligning sequences of multiple isolates to provide relevant information on the diversity and population genetic structure of N. personata to further inform peanut resistance breeding programs and devise the best disease management strategies.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"24 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139816939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-01DOI: 10.1094/phytofr-10-23-0135-a
Maricel Gonzales, Brian L. Abernathy, Robert Kemerait, David Bertioli, Marin Brewer, Soraya Leal-Bertioli
Nothopassalora personata, the causal agent of late leaf spot, is an economically important fungus that poses a significant threat to peanut production worldwide. Currently, studies on N. personata are focused on epidemiology, host resistance, early environmental detection, and molecular studies based on a limited number of genes for classification. A high-quality whole genome sequence can be a valuable tool for studying complex species and identifying molecular mechanisms in pathogenicity and adaptation. This study reports a high-quality, chromosome-scale genome assembly for N. personata with a total length of 54.6 Mb, an N50 of 2.54 Mb, a longest contig length of 4.47 Mb and a BUSCO genome completeness score of 99.5% with mostly single copy genes. Genome annotation revealed 11,295 protein-encoding genes and 12,121 transcripts in which 411 of the 995 predicted proteins were putative effectors. Genome comparison with the closely related fungi Dothistroma septosporum NZE10 and Fulvia fulva (syn. Passalora fulva, Cladosporium fulvum) isolate Race 5 revealed 13 chromosomes. This genome sequence resource can be used as a reference for aligning sequences of multiple isolates to provide relevant information on the diversity and population genetic structure of N. personata to further inform peanut resistance breeding programs and devise the best disease management strategies.
{"title":"Chromosome-scale genome sequence of Nothopassalora personata (syn. Cercosporidium personatum), a devastating fungal pathogen of peanut","authors":"Maricel Gonzales, Brian L. Abernathy, Robert Kemerait, David Bertioli, Marin Brewer, Soraya Leal-Bertioli","doi":"10.1094/phytofr-10-23-0135-a","DOIUrl":"https://doi.org/10.1094/phytofr-10-23-0135-a","url":null,"abstract":"Nothopassalora personata, the causal agent of late leaf spot, is an economically important fungus that poses a significant threat to peanut production worldwide. Currently, studies on N. personata are focused on epidemiology, host resistance, early environmental detection, and molecular studies based on a limited number of genes for classification. A high-quality whole genome sequence can be a valuable tool for studying complex species and identifying molecular mechanisms in pathogenicity and adaptation. This study reports a high-quality, chromosome-scale genome assembly for N. personata with a total length of 54.6 Mb, an N50 of 2.54 Mb, a longest contig length of 4.47 Mb and a BUSCO genome completeness score of 99.5% with mostly single copy genes. Genome annotation revealed 11,295 protein-encoding genes and 12,121 transcripts in which 411 of the 995 predicted proteins were putative effectors. Genome comparison with the closely related fungi Dothistroma septosporum NZE10 and Fulvia fulva (syn. Passalora fulva, Cladosporium fulvum) isolate Race 5 revealed 13 chromosomes. This genome sequence resource can be used as a reference for aligning sequences of multiple isolates to provide relevant information on the diversity and population genetic structure of N. personata to further inform peanut resistance breeding programs and devise the best disease management strategies.","PeriodicalId":508090,"journal":{"name":"PhytoFrontiers™","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139877172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：