Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India
Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resis...
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| creator | Yadav, Inderjit Singh Bhardwaj, S. C Kaur, Jaspal Singla, Deepak Kaur, Satinder Kaur, Harmandeep Rawat, Nidhi Tiwari, Vijay Kumar Saunders, Diane Uauy, Cristobal Chhuneja, Parveen |
| description | Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment. |
| doi_str_mv | 10.1371/journal.pone.0261697 |
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We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0261697</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Alcohol ; Analysis ; Biology and Life Sciences ; Care and treatment ; Computer and Information Sciences ; Diagnosis ; Diseases and pests ; Epidemics ; Evolution ; Evolutionary genetics ; Fungal diseases of plants ; Gene families ; Gene sequencing ; Genes ; Genetic aspects ; Genetic susceptibility ; Genomes ; Growth ; Infections ; Medicine and Health Sciences ; Mutation ; Pathogenicity ; Pathogens ; Phylogeny ; Plant-pathogen relationships ; Positive selection ; Puccinia striiformis ; Races ; Secretome ; Stripe rust ; Testing ; Virulence ; Wheat</subject><ispartof>PloS one, 2022-11, Vol.17 (11), p.e0261697-e0261697</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. 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With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.</description><subject>Alcohol</subject><subject>Analysis</subject><subject>Biology and Life Sciences</subject><subject>Care and treatment</subject><subject>Computer and Information Sciences</subject><subject>Diagnosis</subject><subject>Diseases and pests</subject><subject>Epidemics</subject><subject>Evolution</subject><subject>Evolutionary genetics</subject><subject>Fungal diseases of plants</subject><subject>Gene families</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic susceptibility</subject><subject>Genomes</subject><subject>Growth</subject><subject>Infections</subject><subject>Medicine and Health Sciences</subject><subject>Mutation</subject><subject>Pathogenicity</subject><subject>Pathogens</subject><subject>Phylogeny</subject><subject>Plant-pathogen relationships</subject><subject>Positive selection</subject><subject>Puccinia striiformis</subject><subject>Races</subject><subject>Secretome</subject><subject>Stripe rust</subject><subject>Testing</subject><subject>Virulence</subject><subject>Wheat</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk92K1DAUx4souK6-gWBAEL2Y2jadJrkRlsWPgYUVPy_DaZq0GdqkJungvIDPsc-yT2bGqctW9kJ60XL6O_9zzj85SfI0z9Ick_z11k7OQJ-O1sg0K6q8YuRecpIzXKyqIsP3b30_TB55v82yNaZVdZL8-t7ZXqJWGjtI5KSXPyZphDYtAtMgYYcRHAS9u2EgVtp77ZFVKHROSvRxEjFBA_LBaa2sG7S_vlIp8mN6fRVjQQuNRgidDftRejQ6uYNemoC0QRvTaHicPFDQe_lkfp8mX9-9_XL-YXVx-X5zfnaxElXFwqohWACjoICVuKSMENYwJoRQTV0TzBpCaVUKVZekyRSVmSxpk0OtYE0IbQCfJs-OumNvPZ9987wgOCdZSUocic2RaCxs-ej0AG7PLWj-J2Bdy8HFgXrJ8xqTimSg2BrKKlesrvGaCpzFvmq6LqLWm7naVA-yEXFiB_1CdPnH6I63dsdZhQuKyyjwchZwNp6LDzxaK2Tfg5F2mvvOSUlpRJ__g9493Uy10X-ujbKxrjiI8jNSlLHxqmCRSu-g4tPIQYt4yZSO8UXCq0VCZIL8GVqYvOebz5_-n738tmRf3GI7CX3ovO2noK3xS7A8gsJZ751UNybnGT_syF83-GFH-Lwj-DcrwgjK</recordid><startdate>20221103</startdate><enddate>20221103</enddate><creator>Yadav, Inderjit Singh</creator><creator>Bhardwaj, S. 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C</au><au>Kaur, Jaspal</au><au>Singla, Deepak</au><au>Kaur, Satinder</au><au>Kaur, Harmandeep</au><au>Rawat, Nidhi</au><au>Tiwari, Vijay Kumar</au><au>Saunders, Diane</au><au>Uauy, Cristobal</au><au>Chhuneja, Parveen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India</atitle><jtitle>PloS one</jtitle><date>2022-11-03</date><risdate>2022</risdate><volume>17</volume><issue>11</issue><spage>e0261697</spage><epage>e0261697</epage><pages>e0261697-e0261697</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><doi>10.1371/journal.pone.0261697</doi><tpages>e0261697</tpages><orcidid>https://orcid.org/0000-0002-8599-9479</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Alcohol Analysis Biology and Life Sciences Care and treatment Computer and Information Sciences Diagnosis Diseases and pests Epidemics Evolution Evolutionary genetics Fungal diseases of plants Gene families Gene sequencing Genes Genetic aspects Genetic susceptibility Genomes Growth Infections Medicine and Health Sciences Mutation Pathogenicity Pathogens Phylogeny Plant-pathogen relationships Positive selection Puccinia striiformis Races Secretome Stripe rust Testing Virulence Wheat |
| title | Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India |
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