relationship between phylogenetic distribution and genomic features in neurospora crassa系统发育分布和粗糙脉孢菌基因组特性之间的关系.pdfVIP

Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa 1,2 3 1 Takao Kasuga *, Gertrud Mannhaupt , N. Louise Glass 1 Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America, 2 United States Department of Agriculture - Agricultural Research Service, Department of Plant Pathology, University of California Davis, Davis, California, United States of America, 3 Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Neuherberg, Germany Abstract In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genome data. We demonstrate that an evolutionary approach, which is independent of functional annotation, has great potential as a tool for genome analysis. We chose the genome of a model filamentous fungus Neurospora crassa as an example. Phylogenetic distribution of each predicted protein coding gene (PCG) in the N. crassa genome was used to classify genes into six mutually exclusive lineage specificity (LS) groups, i.e. Eukaryote/Prokaryote-core, Dikarya-core, Ascomycota-core, Pezizomycotina-specific, N. crassa-orphans and Others. Functional category analysis revealed that only ,23% of PCGs in the two most highly lineage-specific grouping, Pezizomycotina-specific and N. crassa-orphans, have functional annotation. In contrast, ,76% of PCGs in the remaining four LS groups have functional annotation. Analysis of chromosomal localization of N. crassa-orphan PCGs and genes encoding for secreted proteins showed enrichment in subtelome