Genome Research, Vol. 10, pp. 416-430
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Department of Biology, University of New Mexico, Albuquerque, NM 87131 (E.L.B, M.A.N., D.O.N.);
National Center for Genome Resources, Santa Fe, New Mexico 87505 (E.L.B.); and
Department of Molecular Genetics and Microbiology,School of Medicine, University of New Mexico,
Albuquerque, New Mexico 87131 (A.L.H.)
E.L.B. is currently in the Department of Zoology
at the University of Florida.
We report a large-scale comparison of sequence data from the
filamentous fungus Neurospora crassa with the complete genome sequence of Saccharomyces cerevisiae. N. crassa is
considerably more morphologically and developmentally complex than
S. cerevisiae. We found that N. crassa has a much
higher proportion of "orphan" genes than S. cerevisiae,
suggesting that its morphological complexity reflects the acquisition
or maintenance of novel genes, consistent with its larger genome. Our
results also indicate the loss of specific genes from S. cerevisiae. Surprisingly, some of the genes lost from S. cerevisiae are involved in basic cellular processes, including
translation and ion (especially calcium) homeostasis. Horizontal gene
transfer from prokaryotes appears to have played a relatively modest
role in the evolution of the N. crassa genome. Differences in
the overall rate of molecular evolution between N. crassa and
S. cerevisiae were not detected. Our results indicate that the
current public sequence databases have fairly complete samples of gene
families with ancient conserved regions, suggesting that further
sequencing will not substantially change the proportion of genes with
homologs among distantly related groups. Models of the evolution of
fungal genomes compatible with these results, and their functional
implications, are discussed.