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dc.contributor.authorSperscneider, J.
dc.contributor.authorGardiner, D.
dc.contributor.authorTaylor, J.
dc.contributor.authorHane, James
dc.contributor.authorSingh, K.
dc.contributor.authorManners, J.
dc.date.accessioned2017-01-30T11:28:43Z
dc.date.available2017-01-30T11:28:43Z
dc.date.created2014-10-08T01:14:48Z
dc.date.issued2013
dc.identifier.citationSperscneider, J. and Gardiner, D. and Taylor, J. and Hane, J. and Singh, K. and Manners, J. 2013. A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi. BMC Genomics. 14.
dc.identifier.urihttp://hdl.handle.net/20.500.11937/12098
dc.description.abstract

Background: Fungal pathogens cause devastating losses in economically important cereal crops by utilisingpathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus farbeen identified by selecting small, cysteine-rich peptides from the secretome despite increasing evidence that notall effectors share these attributes.Results: We take advantage of the availability of sequenced fungal genomes and present an unbiased method forfinding putative pathogen proteins and secreted effectors in a query genome via comparative hidden Markov modelanalyses followed by unsupervised protein clustering. Our method returns experimentally validated fungal effectors inStagonospora nodorum and Fusarium oxysporum as well as the N-terminal Y/F/WxC-motif from the barley powderymildew pathogen. Application to the cereal pathogen Fusarium graminearum reveals a secreted phosphorylcholinephosphatase that is characteristic of hemibiotrophic and necrotrophic cereal pathogens and shares an ancient selectionprocess with bacterial plant pathogens. Three F. graminearum protein clusters are found with an enriched secretionsignal. One of these putative effector clusters contains proteins that share a [SG]-P-C-[KR]-P sequence motif in theN-terminal and show features not commonly associated with fungal effectors. This motif is conserved in secretedpathogenic Fusarium proteins and a prime candidate for functional testing.Conclusions: Our pipeline has successfully uncovered conservation patterns, putative effectors and motifs offungal pathogens that would have been overlooked by existing approaches that identify effectors as small, secreted,cysteine-rich peptides. It can be applied to any pathogenic proteome data, such as microbial pathogen data of plantsand other organisms.

dc.publisherBiomed Central Ltd
dc.relation.urihttp://www.biomedcentral.com/1471-2164/14/807
dc.subjectProtein structure
dc.subjectFungal pathogens
dc.subjectHidden Markov - model
dc.subjectEffectors
dc.subjectCereal host
dc.subjectFusarium graminearum
dc.subjectComparative genomics
dc.titleA comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi
dc.typeJournal Article
dcterms.source.volume14
dcterms.source.issn14712164
dcterms.source.titleBMC Genomics
curtin.accessStatusFulltext not available


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