Elusive origins of the extra genes in Aspergillus oryzae.

PloS One
Nora Khaldi, Kenneth H Wolfe

Abstract

The 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 showe...Continue Reading

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Citations

Jul 27, 2010·PloS One·Erica M Larson, Alexander Idnurm
Nov 16, 2010·Eukaryotic Cell·Gary P MoranDerek J Sullivan
Mar 20, 2009·Current Genetics·Skander Elleuche, Stefanie Pöggeler
Oct 23, 2012·Trends in Microbiology·John G Gibbons, Antonis Rokas
Jul 1, 2011·International Journal of Evolutionary Biology·Nora Khaldi, Kenneth H Wolfe
Aug 8, 2013·Mycologia·Matthew A CampbellJason C Slot
Nov 25, 2011·FEMS Microbiology Letters·David A Fitzpatrick
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Feb 22, 2011·Current Biology : CB·Thomas A Richards
Sep 22, 2010·Fungal Genetics and Biology : FG & B·A John Clutterbuck

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Datasets Mentioned

BETA
AP007150-AP007177

Software Mentioned

BLASTP
yn00
PAML package
ClustalW
PHYML
Gblocks

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