Relationship between phylogenetic distribution and genomic features in Neurospora crassa

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.

Figure 1. Lineage specificity classification of predicted N. crassa protein coding gene (PCG) set based on phylogenetic distribution.

A black circle indicates that the gene homolog is present in the corresponding lineage; a white circle means it is absent. Number of PCGs in each LS group is shown at the bottom. Note that N. crassa is a member of the class Sordariomycetes, which is within the Pezizomycotina.

Figure 2. Proportion of lineage specificity (LS) groups in relation to threshold values for length-adjusted percent protein identity.

The 9,127 N. crassa gene set was classified into five LS groups according to presence/absence of homologs in defined taxonomical units at the given percent protein identity threshold level (25%, 30% or 35%). From the top, the proportion of genes in N. crassa-orphan, Pezizo-specific, Ascomycota-core, Dikarya-core, Euk/Prok-core, and Others LS groups are shown. Note that the number of genes in N. crassa-orphans and Pezizo-specific groups increases and the threshold level rises from 25% to 35%.

Figure 3. Histograms showing the relationship of percent protein identity scores between N. crassa and C. globosum and the number (A) and percentage (B) of protein coding genes (PCGs) in each of the lineage specificity (LS) groups.

Note that the Pezizo-specific group is larger in the bins of lower protein percent identity as compared to the Euk/Prok-core genes, which is significantly higher in the bins of high protein identity.

Figure 4. Distribution of A) N. crassa-orphan, B) Pezizomycotina-specific and C) secretory PCGs across the seven chromosomes.

Distribution of these gene sets were evaluated for every 20 PCGs along N. crassa chromosomes I to VII. The chromosomal distribution of tandemly duplicated N. crassa-orphan PCGs is shown at the lower panel in A). The vertical grey arrows indicate clusters of five or more gene paralogs. Boundaries between chromosomes are shown with vertical lines. A mean density+3 standard deviations (p = 0.001) according to binomial distribution is shown with a horizontal black arrow in each panel.

Figure 5. 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/).