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Relationship between phylogenetic distribution and genomic features in Neurospora crassa.

Kasuga T, Mannhaupt G, Glass NL - PLoS ONE (2009)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.

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 approximately 23% of PCGs in the two most highly lineage-specific grouping, Pezizomycotina-specific and N. crassa-orphans, have functional annotation. In contrast, approximately 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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Examples of gene organization of tandem paralogous pairs of                                N. crassa-orphan PCGs.A) a paralogous gene pair, NCU08102 and NCU08103, shows a head-to-tail                            gene organization; 73 paralogous PCG pairs have this conformation. B)                            NCU08797 and NCU08796 are one of five cases of paralogous gene pairs                            having a head-to-head gene organization. C) NCU05920 and NCU05921 are                            one of four pairs of paralogous genes that show a tail-to-tail gene                            organization. Schematic representations are derived from the MIPS                                Neurospora crassa DataBase (http://mips.gsf.de/genre/proj/ncrassa/).
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pone-0005286-g005: Examples of gene organization of tandem paralogous pairs of N. crassa-orphan PCGs.A) a paralogous gene pair, NCU08102 and NCU08103, shows a head-to-tail gene organization; 73 paralogous PCG pairs have this conformation. B) NCU08797 and NCU08796 are one of five cases of paralogous gene pairs having a head-to-head gene organization. C) NCU05920 and NCU05921 are one of four pairs of paralogous genes that show a tail-to-tail gene organization. Schematic representations are derived from the MIPS Neurospora crassa DataBase (http://mips.gsf.de/genre/proj/ncrassa/).

Mentions: We then examined the relative orientation of consecutive paralogous gene pairs. Of the 82 Orph:Orph paralogous duplication PCG pairs, 73 showed the head-to-tail conformation, while 4 of the paralogous duplication pairs showed a tail-to-tail and 5 had a head-to-head organization (Fig. 5). In the entire N. crassa genome, only 44% of neighboring PCGs have a head-to-tail organization. Given the genome statistics, the head-to-tail organization was enriched in Orph:Orph paralogous PCG duplication pairs (p = 1.6×10−17 by binomial probability). Likewise, although, there were only 6 Orph:Non paralogous consecutive pairs in the genome, 4 of them showed a head-to-tail conformation. Taken together, this enrichment of consecutive paralogous PCG pairs and their head-to-tail organization indicate involvement of tandem duplication events for the generation of N. crassa-orphan genes.


Relationship between phylogenetic distribution and genomic features in Neurospora crassa.

Kasuga T, Mannhaupt G, Glass NL - PLoS ONE (2009)

Examples of gene organization of tandem paralogous pairs of                                N. crassa-orphan PCGs.A) a paralogous gene pair, NCU08102 and NCU08103, shows a head-to-tail                            gene organization; 73 paralogous PCG pairs have this conformation. B)                            NCU08797 and NCU08796 are one of five cases of paralogous gene pairs                            having a head-to-head gene organization. C) NCU05920 and NCU05921 are                            one of four pairs of paralogous genes that show a tail-to-tail gene                            organization. Schematic representations are derived from the MIPS                                Neurospora crassa DataBase (http://mips.gsf.de/genre/proj/ncrassa/).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2684829&req=5

pone-0005286-g005: Examples of gene organization of tandem paralogous pairs of N. crassa-orphan PCGs.A) a paralogous gene pair, NCU08102 and NCU08103, shows a head-to-tail gene organization; 73 paralogous PCG pairs have this conformation. B) NCU08797 and NCU08796 are one of five cases of paralogous gene pairs having a head-to-head gene organization. C) NCU05920 and NCU05921 are one of four pairs of paralogous genes that show a tail-to-tail gene organization. Schematic representations are derived from the MIPS Neurospora crassa DataBase (http://mips.gsf.de/genre/proj/ncrassa/).
Mentions: We then examined the relative orientation of consecutive paralogous gene pairs. Of the 82 Orph:Orph paralogous duplication PCG pairs, 73 showed the head-to-tail conformation, while 4 of the paralogous duplication pairs showed a tail-to-tail and 5 had a head-to-head organization (Fig. 5). In the entire N. crassa genome, only 44% of neighboring PCGs have a head-to-tail organization. Given the genome statistics, the head-to-tail organization was enriched in Orph:Orph paralogous PCG duplication pairs (p = 1.6×10−17 by binomial probability). Likewise, although, there were only 6 Orph:Non paralogous consecutive pairs in the genome, 4 of them showed a head-to-tail conformation. Taken together, this enrichment of consecutive paralogous PCG pairs and their head-to-tail organization indicate involvement of tandem duplication events for the generation of N. crassa-orphan genes.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.

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 approximately 23% of PCGs in the two most highly lineage-specific grouping, Pezizomycotina-specific and N. crassa-orphans, have functional annotation. In contrast, approximately 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.

Show MeSH
Related in: MedlinePlus