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Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes

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Abstract

The purpose of this research was to search for evolutionarily conserved fungal sequences to test the hypothesis that fungi have a set of core genes that are not found in other organisms, as these genes may indicate what makes fungi different from other organisms. By comparing 6355 predicted or known yeast (Saccharomyces cerevisiae) genes to the genomes of 13 other fungi using Standalone TBLASTN at an e-value <1E-5, a list of 3340 yeast genes was obtained with homologs present in at least 12 of 14 fungal genomes. By comparing these common fungal genes to complete genomes of animals (Fugu rubripes, Caenorhabditis elegans), plants (Arabidopsis thaliana, Oryza sativa), and bacteria (Agrobacterium tumefaciens, Xylella fastidiosa), a list of common fungal genes with homologs in these plants, animals, and bacteria was produced (938 genes), as well as a list of exclusively fungal genes without homologs in these other genomes (60 genes). To ensure that the 60 genes were exclusively fungal, these were compared using TBLASTN to the major sequence databases at GenBank: NR (nonredundant), EST (expressed sequence tags), GSS (genome survey sequences), and HTGS (unfinished high-throughput genome sequences). This resulted in 17 yeast genes with homologs in other fungal genomes, but without known homologs in other organisms. These 17 core, fungal genes were not found to differ from other yeast genes in GC content or codon usage patterns. More intensive study is required of these 17 genes and other common fungal genes to discover unique features of fungi compared to other organisms.

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Acknowledgments

This research was initiated while T. Hsiang was on Research Leave at Simon Fraser University working with D.L. Baillie. The authors are very grateful to Z. Punja for providing office space and arranging access to the SFU library and Internet for T. Hsiang, as well as the fruitful discussions with him regarding fungal genomics. We are also very grateful to P.H. Goodwin and J.T. Trevors for their helpful comments on the manuscript.

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Authors and Affiliations

  1. Department of Environmental Biology, University of Guelph, Guelph, Ontario, NIG 2W1, Canada

    Tom Hsiang

  2. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C., V5A 1S6, Canada

    David L. Baillie

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  1. Tom Hsiang
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Correspondence to Tom Hsiang.

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Reviewing Editor: Prof. David Gottman

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Hsiang, T., Baillie, D.L. Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes. J Mol Evol 60, 475–483 (2005). https://doi.org/10.1007/s00239-004-0218-1

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  • DOI: https://doi.org/10.1007/s00239-004-0218-1

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