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Vol. 10, Issue 4, 416-430, April 2000

Large-Scale Comparison of Fungal Sequence Information: Mechanisms of Innovation in Neurospora crassa and Gene Loss in Saccharomyces cerevisiae

Edward L. Braun,1,2,4,5 Aaron L. Halpern,3,4,6 Mary Anne Nelson,1 and Donald O. Natvig1

1 Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131 USA; 2 National Center for Genome Resources, Santa Fe, New Mexico 87505 USA; 3 Department of Molecular Genetics and Microbiology, School of Medicine, University of New Mexico, Albuquerque, New Mexico 87131 USA

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.

4 These authors contributed equally to this paper and should be considered cofirst authors.

5 Present address: Department of Plant Biology, The Ohio State University, Columbus, Ohio 43210 USA.

6 Corresponding author. Present address: Celera Genomics, Rockville Maryland 20850 USA.

10:416-430 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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