title: Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system.
abstract: BACKGROUND
  Adaptive processes shape the evolution of genomes and the diverse functions of different genomic regions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesis of this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomic region 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 a species, when studying populations within a species, and when comparing closely related sister taxa. By coupling a genome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis of intra- and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare and H. 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- and tetranucleotides, 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 species compared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regions they are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic than those in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolution undergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regions involved in regulatory functions.
  
  
  CONCLUSIONS
  Our work linked the variation and the type of SSRs with regions upstream 5'UTR, putatively harbouring regulatory 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 environment mediated by SSRs.
authors.affiliation: Department of Agricultural, Forest and Food Sciences, University of Torino, 10095, Grugliasco, Italy. paolo.gonthier@unito.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Gonthier
authors.affiliation: Department of Agricultural, Forest and Food Sciences, University of Torino, 10095, Grugliasco, Italy. fabiano.sillo@unito.it.
authors.forename: Fabiano
authors.initials: F
authors.lastname: Sillo
authors.affiliation: Department of Environmental Sciences, Policy and Management, University of California at Berkeley, CA, 94720, Berkeley, USA. elisa.lagostina@gmail.com.|Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy. elisa.lagostina@gmail.com.
authors.forename: Elisa
authors.initials: E
authors.lastname: Lagostina
authors.affiliation: Department of Environmental Sciences, Policy and Management, University of California at Berkeley, CA, 94720, Berkeley, USA. aroccotelli@yahoo.it.|Department of Agriculture, Mediterranean University of Reggio Calabria, 89122, Reggio Calabria, Italy. aroccotelli@yahoo.it.
authors.forename: Angela
authors.initials: A
authors.lastname: Roccotelli
authors.affiliation: Department of Agriculture, Food and Environment, University of Catania, 95123, Catania, Italy. olgacacciola@unict.it.
authors.forename: Olga Santa
authors.initials: OS
authors.lastname: Cacciola
authors.affiliation: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden. Jan.Stenlid@slu.se.
authors.forename: Jan
authors.initials: J
authors.lastname: Stenlid
authors.affiliation: Department of Environmental Sciences, Policy and Management, University of California at Berkeley, CA, 94720, Berkeley, USA. matteog@berkeley.edu.
authors.forename: Matteo
authors.initials: M
authors.lastname: Garbelotto
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D018895:Microsatellite Repeats / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions