Molecular evolution of meiosis genes in fungi

Meiosis as a general process is prevalent across the eukaryotes, as are the orthologs of many genes encoding proteins known to function in meiosis. However, many organisms have experienced derived losses of otherwise well-conserved meiosis genes without losing meiosis and sexual reproduction. Although this general conservation of meiosis genes and precedent for derived meiosis gene losses has been previously established, questions remain about the frequency of and evolutionary forces contributing to these trends. This work sought (i) to characterize the phylogenetic distribution of 15 meiosis genes (most of which are known to function only in meiosis) in the exemplar eukaryotic kingdom Fungi and (ii) to use this dataset to investigate evolutionary processes contributing to the loss and retention of these genes.

Orthologs of 15 meiosis genes (Rad51, Rad21, Spo11, Rec8, Dmc1, Hop2, Mnd1, Sae3/Swi5, Mei5/Sfr1, Pch2, Hop1, Msh4, Msh5, Mer3, Zip3) were identified by BLAST-based techniques and phylogenetically validated in most of the 109 publicly available sequenced fungal genomes investigated, but numerous putative derived losses were also detected. Rad51, Rad21, Rec8, and Spo11 were nearly universally conserved; the remaining genes were each undetectable or independently pseudogenized multiple times within fungi, particularly often for Pch2. Genes with previously known functional interactions tended to show parallel presence, absence, or pseudogenization patterns. Although this work primarily established the conserved presence of meiosis gene orthologs at the DNA level, examination of expressed sequence tags (ESTs) showed that many species--including some not previously known to undergo sexual reproduction--were competent to transcribe (and often splice) mRNA from the identified meiosis genes.

Factors potentially influencing derived meiosis gene losses were investigated in two ways. First, degenerate PCR was used to amplify loci expected to contain orthologs of Msh4, Msh5, Pch2, and Zip3 in various Aspergillus species closely related to Aspergillus nidulans (a species with undetected or pseudogenized orthologs of these four genes.) The loss of Pch2 substantially predated the pseudogenization of Msh4, Msh5, and Zip3. Evolutionary rate analyses using the Ka/Ks ratio found no change in nonsynonymous substitution patterns in Msh4 and Msh5 in species that had lost Pch2 compared to those retaining Pch2. Elevated Zip3 Ka/Ks values were found in species with pseudogenized Msh4 and Msh5, suggesting possible obligate functional interactions of Zip3 with Msh4 and Msh5. Second, phylogenetically independent contrasts (PIC) analyses were performed on species from the 109-taxon inventory with published chromosome number and chromosome size estimates to investigate whether changes in either parameter were consistently associated with changes in the presence or absence of meiosis genes. Many analyses had low statistical power, neither detecting nor being able to exclude an association between gene loss and the tested variables. However, several comparisons did detect significant or nearly significant trends: for example, fungi that had lost genes related to crossover interference (Msh4, Msh5, or Pch2) tended to have fewer and/or larger chromosomes than their closest relatives without gene loss.

A final objective was to determine the distribution of meiosis genes in lichenized fungi and green algae to see whether this form of symbiosis was associated with differences in the presence or molecular evolution of meiosis genes. Rad51, Dmc1, and Mnd1 were each amplified by degenerate PCR from multiple lichenized fungi that lacked sequenced genomes, and no systematic difference in evolutionary rate was found between examined lichenized fungi compared to other examined classes in phylum Ascomycota. Bioinformatic analyses of meiosis gene distribution in green algae revealed not only no obvious increased tendency for derived gene losses in examined lichenized green algae but also very few derived meiosis gene losses in green algae in general. This suggests that lichenization may not be associated with consistent differences in the evolution of meiosis genes in either fungal or green algal symbionts. The green algal results also illustrate the need to investigate the extent to which eukaryotes as a whole exhibit the same trends of meiosis gene evolution described here for fungi: frequent derived losses of meiosis genes, genes encoding proteins with function interactions showing similar distributions, likely roles for post-transcriptional regulation of meiosis gene transcripts, and loss of crossover distribution-related genes potentially being associated with constraints on chromosome size and/or haploid chromosome number.