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

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.

[1]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[2]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[3]  S. Shuman,et al.  Genetic and Biochemical Analysis of the Functional Domains of Yeast tRNA Ligase* , 2003, Journal of Biological Chemistry.

[4]  Juancarlos Chan,et al.  WormBase: a cross-species database for comparative genomics , 2003, Nucleic Acids Res..

[5]  Sudhir Kumar,et al.  Genomic clocks and evolutionary timescales. , 2003, Trends in genetics : TIG.

[6]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) , 2002, Science.

[7]  James R. Brown,et al.  Antibiotic discovery: is it all in the genes? , 1998 .

[8]  Juan Mata,et al.  Correlations between gene expression and gene conservation in fission yeast. , 2003, Genome research.

[9]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[10]  H. Mewes,et al.  Overview of the yeast genome. , 1997, Nature.

[11]  J. Piškur,et al.  Yeast genome sequencing: the power of comparative genomics , 2004, Molecular microbiology.

[12]  Temple F. Smith,et al.  Comparison of the complete protein sets of worm and yeast: orthology and divergence. , 1998, Science.

[13]  S. Baldauf,et al.  The Deep Roots of Eukaryotes , 2003, Science.

[14]  Nancy F. Hansen,et al.  Genomic evidence for a complete sexual cycle in Candida albicans , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Paul Nurse,et al.  Schizosaccharomyces pombe essential genes: a pilot study. , 2003, Genome research.

[16]  Katherine H. Huang,et al.  Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 , 2004, Nature Biotechnology.

[17]  Dirk Haase,et al.  What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence. , 2003, Nucleic acids research.

[18]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[19]  H. Philippe,et al.  The new phylogeny of eukaryotes. , 2000, Current opinion in genetics & development.

[20]  R. Wilson,et al.  What is finished, and why does it matter. , 2002, Genome research.

[21]  George Newport,et al.  The diploid genome sequence of Candida albicans. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[23]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[24]  A. Weiner,et al.  Another Bridge between Kingdoms: tRNA Splicing in Archaea and Eukaryotes , 1997, Cell.

[25]  M. Nóbrega,et al.  Comparative genomics at the vertebrate extremes , 2004, Nature Reviews Genetics.

[26]  S. Oliver,et al.  Erratum: Overview of the yeast genome , 1997, Nature.

[27]  M. R. Adams,et al.  Comparative genomics of the eukaryotes. , 2000, Science.

[28]  T. Miller.  Systematics and evolution , 1987 .

[29]  E. Mauceli,et al.  The genome sequence of the filamentous fungus Neurospora crassa , 2003, Nature.

[30]  D. Baillie,et al.  Recent progress, developments, and issues in comparative fungal genomics , 2004 .

[31]  Bas E. Dutilh,et al.  The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise , 2004, Journal of Molecular Evolution.

[32]  J A Eisen,et al.  The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58 , 2001, Science.

[33]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[34]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[35]  S. Hedges,et al.  Molecular Evidence for the Early Colonization of Land by Fungi and Plants , 2001, Science.