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Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea

The present study deals with whole genome analysis of Fusarium udum, a wilt causing pathogen of pigeon pea. The de novo assembly identified a total of 16,179 protein-coding genes, of which 11,892 genes (73.50%) were annotated using BlastP and 8,928 genes (55.18%) from KOG annotation. In addition, 5,...

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Autores principales: Srivastava, Alok K., Srivastava, Ruchi, Yadav, Jagriti, Singh, Alok K., Tiwari, Praveen K., Srivastava, Anchal K., Sahu, Pramod K., Singh, Shiv M., Kashyap, Prem Lal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981795/
https://www.ncbi.nlm.nih.gov/pubmed/36876067
http://dx.doi.org/10.3389/fmicb.2023.1066096
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author Srivastava, Alok K.
Srivastava, Ruchi
Yadav, Jagriti
Singh, Alok K.
Tiwari, Praveen K.
Srivastava, Anchal K.
Sahu, Pramod K.
Singh, Shiv M.
Kashyap, Prem Lal
author_facet Srivastava, Alok K.
Srivastava, Ruchi
Yadav, Jagriti
Singh, Alok K.
Tiwari, Praveen K.
Srivastava, Anchal K.
Sahu, Pramod K.
Singh, Shiv M.
Kashyap, Prem Lal
author_sort Srivastava, Alok K.
collection PubMed
description The present study deals with whole genome analysis of Fusarium udum, a wilt causing pathogen of pigeon pea. The de novo assembly identified a total of 16,179 protein-coding genes, of which 11,892 genes (73.50%) were annotated using BlastP and 8,928 genes (55.18%) from KOG annotation. In addition, 5,134 unique InterPro domains were detected in the annotated genes. Apart from this, we also analyzed genome sequence for key pathogenic genes involved in virulence, and identified 1,060 genes (6.55%) as virulence genes as per the PHI-BASE database. The secretome profiling of these virulence genes indicated the presence of 1,439 secretory proteins. Of those, an annotation of 506 predicted secretory proteins through CAZyme database indicated maximum abundance of Glycosyl hydrolase (GH, 45%) family proteins followed by auxiliary activity (AA) family proteins. Interestingly, the presence of effectors for cell wall degradation, pectin degradation, and host cell death was found. The genome comprised approximately 895,132 bp of repetitive elements, which includes 128 long terminal repeats (LTRs), and 4,921 simple sequence repeats (SSRs) of 80,875 bp length. The comparative mining of effector genes among different Fusarium species revealed five common and two specific effectors in F. udum that are related to host cell death. Furthermore, wet lab experiment validated the presence of effector genes like SIX (for Secreted in Xylem). We conclude that deciphering the whole genome of F. udum would be instrumental in understanding evolution, virulence determinants, host-pathogen interaction, possible control strategies, ecological behavior, and many other complexities of the pathogen.
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spelling pubmed-99817952023-03-04 Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea Srivastava, Alok K. Srivastava, Ruchi Yadav, Jagriti Singh, Alok K. Tiwari, Praveen K. Srivastava, Anchal K. Sahu, Pramod K. Singh, Shiv M. Kashyap, Prem Lal Front Microbiol Microbiology The present study deals with whole genome analysis of Fusarium udum, a wilt causing pathogen of pigeon pea. The de novo assembly identified a total of 16,179 protein-coding genes, of which 11,892 genes (73.50%) were annotated using BlastP and 8,928 genes (55.18%) from KOG annotation. In addition, 5,134 unique InterPro domains were detected in the annotated genes. Apart from this, we also analyzed genome sequence for key pathogenic genes involved in virulence, and identified 1,060 genes (6.55%) as virulence genes as per the PHI-BASE database. The secretome profiling of these virulence genes indicated the presence of 1,439 secretory proteins. Of those, an annotation of 506 predicted secretory proteins through CAZyme database indicated maximum abundance of Glycosyl hydrolase (GH, 45%) family proteins followed by auxiliary activity (AA) family proteins. Interestingly, the presence of effectors for cell wall degradation, pectin degradation, and host cell death was found. The genome comprised approximately 895,132 bp of repetitive elements, which includes 128 long terminal repeats (LTRs), and 4,921 simple sequence repeats (SSRs) of 80,875 bp length. The comparative mining of effector genes among different Fusarium species revealed five common and two specific effectors in F. udum that are related to host cell death. Furthermore, wet lab experiment validated the presence of effector genes like SIX (for Secreted in Xylem). We conclude that deciphering the whole genome of F. udum would be instrumental in understanding evolution, virulence determinants, host-pathogen interaction, possible control strategies, ecological behavior, and many other complexities of the pathogen. Frontiers Media S.A. 2023-02-17 /pmc/articles/PMC9981795/ /pubmed/36876067 http://dx.doi.org/10.3389/fmicb.2023.1066096 Text en Copyright © 2023 Srivastava, Srivastava, Yadav, Singh, Tiwari, Srivastava, Sahu, Singh and Kashyap. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Srivastava, Alok K.
Srivastava, Ruchi
Yadav, Jagriti
Singh, Alok K.
Tiwari, Praveen K.
Srivastava, Anchal K.
Sahu, Pramod K.
Singh, Shiv M.
Kashyap, Prem Lal
Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea
title Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea
title_full Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea
title_fullStr Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea
title_full_unstemmed Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea
title_short Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea
title_sort virulence and pathogenicity determinants in whole genome sequence of fusarium udum causing wilt of pigeon pea
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981795/
https://www.ncbi.nlm.nih.gov/pubmed/36876067
http://dx.doi.org/10.3389/fmicb.2023.1066096
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