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Title:   Author  item
                                            Kasuga, Takaoitem
                                            MANNHAUPT, GERTRUD - Institute For Bioinformatics - Germanyitem
                                            GLASS, NANCY - University Of California
  Submitted to: PLOS ONE
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 8/18/2009
                                    Publication  Date: 4/21/2009
                                    Citation: Kasuga, T., Mannhaupt, G., Glass, N.L. 2009. RELATIONSHIP BETWEEN PHYLOGENETIC DISTRIBUTION AND GENOMIC FEATURES IN NEUROSPORA CRASSA. PLoS One. 10.1371/journal.pone.0005286Interpretive Summary: Although genome sequences are available for many organisms, functions of a great number of genes are still unknown (unannotated).  Because of this, at present, utility of genome data is greatly restricted.  We have developed a new approach to utilize the genome data, which does not rely on functional annotations.  We chose the genome of a model filamentous fungus Neurospora crassa (pink bread mold) as an example.  It is known that some genes are evolutionarily conserved among distantly related organisms, such as fungi, plants and animals.  Whereas some genes are shared only within closely related species such as the fungal kingdom, and some genes are unique to a particular species.  We used this information and classified c.a. 9,000 genes in N. crassa into six evolutionary groups.  We demonstrated this gene classification system to be a useful tool in exploring and understanding genome organization and gene function in fungi.
                                Technical 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 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, implying a duplication origin of N. crassa-orphan PCGs in the past.  LS grouping is thus a useful tool to explore and understand genome organization, evolution and gene function in fungi.


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