Subject(s)
Fungi/genetics , Fungi/pathogenicity , Phytophthora/genetics , Phytophthora/pathogenicity , Plant Diseases/microbiology , Algal Proteins/genetics , Amino Acid Sequence , Cluster Analysis , Codon/genetics , DNA, Algal/genetics , DNA, Complementary/genetics , DNA, Fungal/genetics , Evolution, Molecular , Expressed Sequence Tags , Fungi/metabolism , Gene Library , Lysine/biosynthesis , Molecular Sequence Data , Phylogeny , Phytophthora/metabolism , Polysaccharide-Lyases/genetics , Sequence Homology, Amino Acid , Species Specificity , Virulence/geneticsABSTRACT
We have sequenced and annotated the genome of the filamentous ascomycete Ashbya gossypii. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of A. gossypii genes show both homology and a particular pattern of synteny with Saccharomyces cerevisiae. Analysis of this pattern revealed 300 inversions and translocations that have occurred since divergence of these two species. It also provided compelling evidence that the evolution of S. cerevisiae included a whole genome duplication or fusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies.
Subject(s)
Chromosome Mapping , Genome, Fungal , Saccharomyces cerevisiae/genetics , Saccharomycetales/genetics , Sequence Analysis, DNA , Base Composition , Biological Evolution , Centromere/genetics , Chromosome Inversion , Computational Biology , Fungal Proteins/genetics , Gene Duplication , Gene Order , Genes, Fungal , Molecular Sequence Data , Open Reading Frames , Sequence Alignment , Sequence Homology, Nucleic Acid , Synteny , Translocation, GeneticABSTRACT
BACKGROUND: The recently sequenced genome of the filamentous fungus Ashbya gossypii revealed remarkable similarities to that of the budding yeast Saccharomyces cerevisiae both at the level of homology and synteny (conservation of gene order). Thus, it became possible to reinvestigate the S. cerevisiae genome in the syntenic regions leading to an improved annotation. RESULTS: We have identified 23 novel S. cerevisiae open reading frames (ORFs) as syntenic homologs of A. gossypii genes; for all but one, homologs are present in other eukaryotes including humans. Other comparisons identified 13 overlooked introns and suggested 69 potential sequence corrections resulting in ORF extensions or ORF fusions with improved homology to the syntenic A. gossypii homologs. Of the proposed corrections, 25 were tested and confirmed by resequencing. In addition, homologs of nearly 1,000 S. cerevisiae ORFs, presently annotated as hypothetical, were found in A. gossypii at syntenic positions and can therefore be considered as authentic genes. Finally, we suggest that over 400 S. cerevisiae ORFs that overlap other ORFs in S. cerevisiae and for which no homolog can be detected in A. gossypii should be regarded as spurious. CONCLUSIONS: Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, we have shown that it still benefits substantially from comparison to the completed sequence and syntenic gene map of A. gossypii, an evolutionarily related fungus. This type of approach will strongly support the annotation of more complex genomes such as the human and murine genomes.
