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De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen
Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, anno...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547962/ https://www.ncbi.nlm.nih.gov/pubmed/23349770 http://dx.doi.org/10.1371/journal.pone.0053937 |
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author | Thakur, Karnika Chawla, Vandna Bhatti, Shammi Swarnkar, Mohit Kumar Kaur, Jagdeep Shankar, Ravi Jha, Gopaljee |
author_facet | Thakur, Karnika Chawla, Vandna Bhatti, Shammi Swarnkar, Mohit Kumar Kaur, Jagdeep Shankar, Ravi Jha, Gopaljee |
author_sort | Thakur, Karnika |
collection | PubMed |
description | Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction. |
format | Online Article Text |
id | pubmed-3547962 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35479622013-01-24 De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen Thakur, Karnika Chawla, Vandna Bhatti, Shammi Swarnkar, Mohit Kumar Kaur, Jagdeep Shankar, Ravi Jha, Gopaljee PLoS One Research Article Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction. Public Library of Science 2013-01-17 /pmc/articles/PMC3547962/ /pubmed/23349770 http://dx.doi.org/10.1371/journal.pone.0053937 Text en © 2013 Thakur et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Thakur, Karnika Chawla, Vandna Bhatti, Shammi Swarnkar, Mohit Kumar Kaur, Jagdeep Shankar, Ravi Jha, Gopaljee De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen |
title |
De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen |
title_full |
De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen |
title_fullStr |
De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen |
title_full_unstemmed |
De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen |
title_short |
De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen |
title_sort | de novo transcriptome sequencing and analysis for venturia inaequalis, the devastating apple scab pathogen |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547962/ https://www.ncbi.nlm.nih.gov/pubmed/23349770 http://dx.doi.org/10.1371/journal.pone.0053937 |
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