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...

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Autores principales:	Karnika Thakur, Vandna Chawla, Shammi Bhatti, Mohit Kumar Swarnkar, Jagdeep Kaur, Ravi Shankar, Gopaljee Jha
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/eb0a18f19f784b89ba1dd2fea6f69d4d
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spelling	oai:doaj.org-article:eb0a18f19f784b89ba1dd2fea6f69d4d2021-11-18T08:01:05ZDe novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen.1932-620310.1371/journal.pone.0053937https://doaj.org/article/eb0a18f19f784b89ba1dd2fea6f69d4d2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23349770/?tool=EBIhttps://doaj.org/toc/1932-6203Venturia 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.Karnika ThakurVandna ChawlaShammi BhattiMohit Kumar SwarnkarJagdeep KaurRavi ShankarGopaljee JhaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e53937 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Karnika Thakur Vandna Chawla Shammi Bhatti Mohit Kumar Swarnkar Jagdeep Kaur Ravi Shankar Gopaljee Jha De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen.
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	article
author	Karnika Thakur Vandna Chawla Shammi Bhatti Mohit Kumar Swarnkar Jagdeep Kaur Ravi Shankar Gopaljee Jha
author_facet	Karnika Thakur Vandna Chawla Shammi Bhatti Mohit Kumar Swarnkar Jagdeep Kaur Ravi Shankar Gopaljee Jha
author_sort	Karnika Thakur
title	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_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_sort	de novo transcriptome sequencing and analysis for venturia inaequalis, the devastating apple scab pathogen.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/eb0a18f19f784b89ba1dd2fea6f69d4d
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De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen.

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