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

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. Large-Scale Comparison of Fungal Sequence Information: Mechanisms of Innovation in Neurospora crassa and Gene Loss in Saccharomyces cerevisiae Edward L. Braun, Aaron L. Halpern, Mary Anne Nelson, and Donald O. Natvig Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131 USA; National Center for Genome Resources, Santa Fe, New Mexico 87505 USA; 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. Sequence comparisons are often used in comparative genomics to infer sequence/function relationships in one organism based on similarities to sequences in other organisms, but it is also instructive to ask about differences between organisms or their genomes and to ask how such differences arose. We have conducted a large-scale comparison of sequence information from the filamentous fungus Neurospora crassa, the unicellular fungus Saccharomyces cerevisiae, and sequences from nonfungal organisms, to investigate patterns of fungal genome evolution. A large number of N. crassa EST sequences are available (Nelson et al. 1997; this paper), as is the complete genome sequence of S. cerevisiae (Goffeau et al. 1996). N. crassa and S. cerevisiae are ascomycete fungi and are estimated to have diverged from each other at least 310 mya (Berbee and Taylor 1993) and probably >400 mya (Taylor et al. 1999). This represents sufficient time for substantial differences to have arisen, but it is substantially more recent than the divergence of the fungi from other eukaryotes, >1 bya (Knoll 1992; Feng et al. 1997). The N. crassa genome is approximately three times the size of the S. cerevisiae genome. N. crassa also exhibits much greater morphological and developmental complexity (Springer 1993), suggesting that N. crassa has a substantially greater number of genes. The number of genes in N. crassa has been estimated to be 1.5– 2.2 times greater than that of S. cerevisiae (Kupfer et al. 1997; Nelson et al. 1997). A previous analysis of ESTs from N. crassa indicated that it has a much higher proportion of genes without identifiable homologs (commonly designated “orphan” genes) than S. cerevisiae (Nelson et al. 1997), a finding that we demonstrate more rigorously here. These differences in genome size, gene number, phenotypic complexity, and proportion of orphan genes raise various possibilities regarding the evolution of fungal genomes. On the one hand, it is possible that S. cerevisiae has been “streamlined” by the loss of genes, with a corresponding loss of phenotypic complexity (e.g., multicellularity). This hypothesis is consistent with phylogenetic analyses of the fungi that indicate that the unicellular fungi arose from multicellular ancestors (Bruns et al. 1992; Berbee and Taylor 1993; Liu These authors contributed equally to this paper and should be considered cofirst authors. Present address: Department of Plant Biology, The Ohio State University, Columbus, Ohio 43210 USA. Corresponding author. Present address: Celera Genomics, Rockville Maryland 20850 USA. E-MAIL [email protected]; FAX (240) 453-3324. Article 416 Genome Research 10:416–430 ©2000 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/00 $5.00; www.genome.org www.genome.org et al. 1999). Some genes that are present in N. crassa but not in S. cerevisiae do reflect the loss from S. cerevisiae of genes present in the common ancestor of these organisms (Braun et al. 1998). Gene loss might result in a concentration of widely conserved genes that are essential for life (e.g., Mushegian and Koonin 1997; Snel et al. 1999), providing an explanation for the lower proportion of orphan genes in S. cerevisiae. On the other hand, addition of a large number of genes to the N. crassa lineage subsequent to its divergence from the ancestor of S. cerevisiae could also explain the differences in genome size, developmental complexity, and—if the acquired genes were either truly novel or free to diverge radically from their sources—proportions of orphan genes. We reasoned that comparison of N. crassa sequences to the complete S. cerevisiae genome and nonfungal sequence databases would provide us with insights bearing on these alternatives. For instance, genes present both in N. crassa and in other nonfungal eukaryotes but absent from S. cerevisiae are likely to reflect genes that have been lost from the S. cerevisiae lineage. Clearly, such gene losses could have substantial functional significance. Genes that are present in both N. crassa and prokaryotic organisms but not in S. cerevisiae or nonfungal eukaryotes are plausible candidates for horizontal transfer into the N. crassa lineage. If a large number of candidates for gene loss from S. cerevisiae or horizontal transfer into N. crassa were identified, these mechanisms could account for much of the difference in genome sizes and gene numbers between the two fungi. Although examples of both classes were identified by this study, a relatively modest number of candidate lost or transferred genes were identified, indicating that alternative explanations for the differences between N. crassa and S. cerevisiae must be sought.