Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa 英文参考文献.docVIP

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Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa 英文参考文献.doc

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Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa 英文参考文献

RelationshipbetweenPhylogeneticDistributionand GenomicFeaturesinNeurosporacrassa TakaoKasuga1,2*,GertrudMannhaupt3,N.LouiseGlass1 1Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America, 2United States Department of Agriculture - Agricultural Research Service, Department of Plant Pathology, University of California Davis, Davis, California, United States of America, 3Helmholtz Centre Munich, GermanResearchCentreforEnvironmentalHealth(GmbH),InstituteofBioinformaticsandSystemsBiology,Neuherberg,Germany Abstract In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genomedata.Wedemonstratethatanevolutionaryapproach,whichisindependentoffunctionalannotation,hasgreat 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 functionalannotation.Incontrast,,76%ofPCGsintheremainingfourLSgroupshavefunctionalannotation.Analysisof chromosomal localization of N. crassa-orphan PCGs and genes encoding for secreted proteins showed enrichment in subtelomeric regions. The origin of N. crassa-orphans is not known. We found that 11% of N. crassa-orphans have paralogous N. crassa-orphan genes. Of the paralogous N. crassa-orphan gene pairs, 33% were tandemly located in the genome,implyingaduplicationoriginofN.crassa-orphanPCGsinthepast.LSgroupingisthusausefultooltoexploreand understandgenomeorganization,evolutionandgenefunctioninfungi. Citat