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

Gonthier P, Sillo F, Lagostina E, Roccotelli A, Cacciola OS, Stenlid J, Garbelotto M - BMC Genomics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural, Forest and Food Sciences, University of Torino, 10095, Grugliasco, Italy. paolo.gonthier@unito.it.

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.

No MeSH data available.


Related in: MedlinePlus

SSRs distribution across different scaffolds (chromosomes) of the H. irregulare reference genome. The 14 scaffolds corresponding to chromosomes are shown. Gene density (1) in a window size of 20 Kbp is colour coded from light yellow to dark red, with deeper red region representing high gene density. From outer to inner, black histograms represent distribution of hexa- (track 2), penta- (track 3), tetra- (track 4), tri- (track 5), di- (track 6) nucleotidic SSRs, respectively. Histogram size represent frequency of SSRs in a window size of 10 Kbp. Figures were drawn by using Circos software v. 0.64 (http://circos.ca/)
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Fig1: SSRs distribution across different scaffolds (chromosomes) of the H. irregulare reference genome. The 14 scaffolds corresponding to chromosomes are shown. Gene density (1) in a window size of 20 Kbp is colour coded from light yellow to dark red, with deeper red region representing high gene density. From outer to inner, black histograms represent distribution of hexa- (track 2), penta- (track 3), tetra- (track 4), tri- (track 5), di- (track 6) nucleotidic SSRs, respectively. Histogram size represent frequency of SSRs in a window size of 10 Kbp. Figures were drawn by using Circos software v. 0.64 (http://circos.ca/)

Mentions: Based on our search parameters, the total number of perfect SSRs was 2541, representing about 0.0017 % of the H. irregulare genome. There was approximately one microsatellite per 13.26 Kbp and the total numbers of SSRs in intergenic and intragenic regions were similar, 1372 versus 1169 (Fig. 1).Fig. 1


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

Gonthier P, Sillo F, Lagostina E, Roccotelli A, Cacciola OS, Stenlid J, Garbelotto M - BMC Genomics (2015)

SSRs distribution across different scaffolds (chromosomes) of the H. irregulare reference genome. The 14 scaffolds corresponding to chromosomes are shown. Gene density (1) in a window size of 20 Kbp is colour coded from light yellow to dark red, with deeper red region representing high gene density. From outer to inner, black histograms represent distribution of hexa- (track 2), penta- (track 3), tetra- (track 4), tri- (track 5), di- (track 6) nucleotidic SSRs, respectively. Histogram size represent frequency of SSRs in a window size of 10 Kbp. Figures were drawn by using Circos software v. 0.64 (http://circos.ca/)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696308&req=5

Fig1: SSRs distribution across different scaffolds (chromosomes) of the H. irregulare reference genome. The 14 scaffolds corresponding to chromosomes are shown. Gene density (1) in a window size of 20 Kbp is colour coded from light yellow to dark red, with deeper red region representing high gene density. From outer to inner, black histograms represent distribution of hexa- (track 2), penta- (track 3), tetra- (track 4), tri- (track 5), di- (track 6) nucleotidic SSRs, respectively. Histogram size represent frequency of SSRs in a window size of 10 Kbp. Figures were drawn by using Circos software v. 0.64 (http://circos.ca/)
Mentions: Based on our search parameters, the total number of perfect SSRs was 2541, representing about 0.0017 % of the H. irregulare genome. There was approximately one microsatellite per 13.26 Kbp and the total numbers of SSRs in intergenic and intragenic regions were similar, 1372 versus 1169 (Fig. 1).Fig. 1

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural, Forest and Food Sciences, University of Torino, 10095, Grugliasco, Italy. paolo.gonthier@unito.it.

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.

No MeSH data available.


Related in: MedlinePlus