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dc.contributor.authorWOLFE, KENNETH
dc.date.accessioned2010-08-18T10:47:26Z
dc.date.available2010-08-18T10:47:26Z
dc.date.issued2008
dc.date.submitted2008en
dc.identifier.citationKhaldi, N. & Wolfe, K.H, Elusive origins of the extra genes in Aspergillus oryzae, PLoS ONE, 3, 8, 2008, e3036en
dc.identifier.otherY
dc.identifier.urihttp://hdl.handle.net/2262/40512
dc.descriptionPUBLISHEDen
dc.description.abstractThe genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT) from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors.en
dc.description.sponsorshipThis study was supported by Science Foundation Ireland. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.format.extente3036en
dc.language.isoenen
dc.publisherPLoSen
dc.relation.ispartofseriesPLoS ONE;
dc.relation.ispartofseries3;
dc.relation.ispartofseries8;
dc.rightsYen
dc.subjectGeneticsen
dc.subjectAspergillus oryzaeen
dc.titleElusive origins of the extra genes in Aspergillus oryzaeen
dc.typeJournal Articleen
dc.contributor.sponsorScience Foundation Irelanden
dc.type.supercollectionscholarly_publicationsen
dc.type.supercollectionrefereed_publicationsen
dc.identifier.peoplefinderurlhttp://people.tcd.ie/khwolfe
dc.identifier.rssinternalid67482
dc.identifier.rssurihttp://dx.doi.org/10.1371/journal.pone.0003036en


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