| Abstract: | In the post-genome era, insufficient functional annotation of predicted genesgreatly restricts the potential of mining genome data. We demonstrate that anevolutionary approach, which is independent of functional annotation, has greatpotential as a tool for genome analysis. We chose the genome of a modelfilamentous fungus Neurospora crassa as an example.Phylogenetic distribution of each predicted protein coding gene (PCG) in theN. crassa genome was used to classify genes into sixmutually 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 PCGsin the two most highly lineage-specific grouping, Pezizomycotina-specific andN. crassa-orphans, have functional annotation. In contrast,∼76% of PCGs in the remaining four LS groups have functionalannotation. Analysis of chromosomal localization of N.crassa-orphan PCGs and genes encoding for secreted proteins showedenrichment in subtelomeric regions. The origin of N.crassa-orphans is not known. We found that 11% of N.crassa-orphans have paralogous N. crassa-orphangenes. Of the paralogous N. crassa-orphan gene pairs,33% were tandemly located in the genome, implying a duplicationorigin of N. crassa-orphan PCGs in the past. LS grouping isthus a useful tool to explore and understand genome organization, evolution andgene function in fungi. |
