Genome Research, Vol. 10, pp. 416-430
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Large-Scale Comparison of Fungal Sequence Information: Mechanisms of Innovation in Neurospora crassa and Gene Loss in Saccharomyces cerevisiae
Edward L. Braun1,
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. crassagenome. 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.
We are grateful to the Albuquerque High Performance Computing Center (AHPCC) for computers and computational support. NGP sequencing was supported by UNM and NSF grant HRD-9550649 to D.O.N., M.A.N., M. Werner-Washburne, and R. Miller. A.L.H. was supported by NIH grant 5P20-RR11830-02 and the AHPCC.1 These authors contributed equally to this paper.
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