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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 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.

Elusive Origins of the Extra Genes in Aspergillus oryzae