Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

Abstract

Abstract. The evolutionary origin of ''orphan'' genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene's orthologues in related species. Highly lineagespecific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene's evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes.

MP1 Homologue-Based Multilocus Sequence System for Typing the Pathogenic Fungus Penicillium marneffei : a Novel Approach Using Lineage-Specific Genes

“…In fact, the same phenomenon was also observed in bacterial pathogens, and it has been shown that the same discriminatory power can be achieved by using fewer targets, hence decreasing the labor and consumable costs considerably, if nonhousekeeping genes are used (15,28). This is in line with our recent observation that lineage-specific genes were associated with more rapid evolutionary rates (4). Hence, more mutations would be expected in these genes than in housekeeping genes, which are not lineage specific, between different strains.…”

“…Subsequently, we have documented that Mp1p-based enzyme-linked immunosorbent assays for antibody and antigen detection are very useful for serodiagnosis of active P. marneffei infections, and an MP1-based DNA vaccine produced a protective immune response against P. marneffei challenge in a mouse model (6,7,38). Recently, we discovered that genes with higher lineage specificity in Ascomycetes evolved at a much faster rate than those with lower lineage specificity (4). Therefore, genes with higher lineage specificity are potentially more useful targets than housekeeping genes for typing pathogenic fungi.…”

Novel Pan-Genomic Analysis Approach in Target Selection for Multiplex PCR Identification and Detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia Complex Species: a Proof-of-Concept Study

“…A three-step approach was devised from our previous publication on lineage-specific genes (8). First, predicted protein sequences for the sequenced genomes of B. pseudomallei, B. thailandensis, and the B. cepacia complex were downloaded from the NCBI Genome database (www.ncbi.nlm.nih.gov/sites/genome).…”

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

“…Although the emergence and evolution of CLS transcripts is not clear, it may be speculated that these genes might have appeared in the Fabaceae after their divergence from non-Fabaceae plants or they may have been lost in nonFabaceae plants after their divergence from the Fabaceae plants. In addition, several hypotheses, including lateral gene transfer, gene duplication followed by sequence divergence, enhanced evolutionary rate, and de novo emergence of genes for noncoding DNA, have been proposed for the evolution of lineage-specific genes (Daubin et al, 2003;Cai et al, 2006;Levine et al, 2006).…”