Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.

The identification of virulence genes in plant pathogenic fungi is important for understanding the infection process, host range and for developing control strategies. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give...

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Autores principales:	Artem Lysenko, Martin Urban, Laura Bennett, Sophia Tsoka, Elzbieta Janowska-Sejda, Chris J Rawlings, Kim E Hammond-Kosack, Mansoor Saqi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c5c856f85ae548aa82103563e17c8256
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spelling	oai:doaj.org-article:c5c856f85ae548aa82103563e17c82562021-11-18T07:38:33ZNetwork-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.1932-620310.1371/journal.pone.0067926https://doaj.org/article/c5c856f85ae548aa82103563e17c82562013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23861834/?tool=EBIhttps://doaj.org/toc/1932-6203The identification of virulence genes in plant pathogenic fungi is important for understanding the infection process, host range and for developing control strategies. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a 'guilt by association' approach. Here we study 133 genes in the globally important Ascomycete fungus Fusarium graminearum that have been experimentally tested for their involvement in virulence. An integrated network that combines information from gene co-expression, predicted protein-protein interactions and sequence similarity was employed and, using 100 genes known to be required for virulence, we found a total of 215 new proteins potentially associated with virulence of which 29 are annotated as hypothetical proteins. The majority of these potential virulence genes are located in chromosomal regions known to have a low recombination frequency. We have also explored the taxonomic diversity of these candidates and found 25 sequences, which are likely to be fungal specific. We discuss the biological relevance of a few of the potentially novel virulence associated genes in detail. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a 'guilt by association' approach.Artem LysenkoMartin UrbanLaura BennettSophia TsokaElzbieta Janowska-SejdaChris J RawlingsKim E Hammond-KosackMansoor SaqiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e67926 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Artem Lysenko Martin Urban Laura Bennett Sophia Tsoka Elzbieta Janowska-Sejda Chris J Rawlings Kim E Hammond-Kosack Mansoor Saqi Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
description	The identification of virulence genes in plant pathogenic fungi is important for understanding the infection process, host range and for developing control strategies. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a 'guilt by association' approach. Here we study 133 genes in the globally important Ascomycete fungus Fusarium graminearum that have been experimentally tested for their involvement in virulence. An integrated network that combines information from gene co-expression, predicted protein-protein interactions and sequence similarity was employed and, using 100 genes known to be required for virulence, we found a total of 215 new proteins potentially associated with virulence of which 29 are annotated as hypothetical proteins. The majority of these potential virulence genes are located in chromosomal regions known to have a low recombination frequency. We have also explored the taxonomic diversity of these candidates and found 25 sequences, which are likely to be fungal specific. We discuss the biological relevance of a few of the potentially novel virulence associated genes in detail. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a 'guilt by association' approach.
format	article
author	Artem Lysenko Martin Urban Laura Bennett Sophia Tsoka Elzbieta Janowska-Sejda Chris J Rawlings Kim E Hammond-Kosack Mansoor Saqi
author_facet	Artem Lysenko Martin Urban Laura Bennett Sophia Tsoka Elzbieta Janowska-Sejda Chris J Rawlings Kim E Hammond-Kosack Mansoor Saqi
author_sort	Artem Lysenko
title	Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
title_short	Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
title_full	Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
title_fullStr	Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
title_full_unstemmed	Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
title_sort	network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus fusarium graminearum.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/c5c856f85ae548aa82103563e17c8256
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Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.

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