Selection processes in simple sequence repeats suggest a correlation with their genomic location: Insights from a fungal model system

Background: Adaptive processes shape the evolution of genomes and the diverse functions of different genomicregions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesisof this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomicregion in which they are located, resulting in differences of motif size, number of repeats, and levels of polymorphisms.These differences should be clearly detectable when analyzing the frequency and type of SSRs within the genome of aspecies, when studying populations within a species, and when comparing closely related sister taxa. By coupling agenome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis ofintra- and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare andH. annosum, we investigated mechanisms of evolution of SSRs.Results: Results showed a clear dominance of trirepeats and a selection against other repeat number, i.e. di- andtetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 5’ untranslated region (5’UTR).Locus per locus AMOVA showed SSRs both inside ORFs and upstream 5’UTR were more conserved within speciescompared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regionsthey are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic thanthose in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolutionundergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regionsinvolved in regulatory functions.Conclusions: Our work linked the variation and the type of SSRs with regions upstream 5’UTR, putatively harbouringregulatory elements, and shows that the evolution of SSRs might be affected by their location in the genome.Additionally, this study provides a first glimpse on a possible molecular basis for fast adaptation to the environmentmediated by SSRs.