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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

PCoA scatter plots showing the genetic distance among genotypes. Genotypes of H. irregulare (LZO5-IR, LZO6-IR) from 2 distinct sampling populations, both from Latium, and genotypes of H. annosum (PVA-AN, EMR-AN, LZO-AN) belonging to 3 distinct sampling populations from various regions of Northern and central Italy, including Latium, were considered
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Fig6: PCoA scatter plots showing the genetic distance among genotypes. Genotypes of H. irregulare (LZO5-IR, LZO6-IR) from 2 distinct sampling populations, both from Latium, and genotypes of H. annosum (PVA-AN, EMR-AN, LZO-AN) belonging to 3 distinct sampling populations from various regions of Northern and central Italy, including Latium, were considered

Mentions: AMOVAs were performed on 51 Heterobasidion genotypes from two H. irregulare and three H. annosum populations. Results including all loci indicated that most of the genetic variability (54–71 %) was among genotypes within population, 3–9 % of the genetic variance was among populations within species, and 25–43 % of the molecular variance was between the two species (Table 3). Averaging all loci and populations, Fst values were as high as 0.40 (SD 0.22, p-value  < 0.05). Average Fst values by each of the abovementioned categories were as follows: 0.37 for OUT loci, 0.42 for UP loci, 0.45 for IN loci, and 0.30 for DOWN loci. Details on percentage of per locus variance, as well as Fst and gene flow (2 Nm) values, calculated considering the genotypes as haploids, are summarized in Fig. 5 and Additional file 2, respectively. The genetic diversity detected with the 39 loci was sufficiently informative to reflect the genetic distinction between species. The PCoA showed a clear genetic differentiation between H. irregulare and H. annosum, especially when UP and IN loci were considered (Fig. 6). In IN loci no overlap between species was observed, while in OUT, UP, and DOWN loci partial overlap was observed between H. irregulare genotypes and H. annosum genotypes from the Latium population (LZO-AN) (Fig. 6).Table 3


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)

PCoA scatter plots showing the genetic distance among genotypes. Genotypes of H. irregulare (LZO5-IR, LZO6-IR) from 2 distinct sampling populations, both from Latium, and genotypes of H. annosum (PVA-AN, EMR-AN, LZO-AN) belonging to 3 distinct sampling populations from various regions of Northern and central Italy, including Latium, were considered
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: PCoA scatter plots showing the genetic distance among genotypes. Genotypes of H. irregulare (LZO5-IR, LZO6-IR) from 2 distinct sampling populations, both from Latium, and genotypes of H. annosum (PVA-AN, EMR-AN, LZO-AN) belonging to 3 distinct sampling populations from various regions of Northern and central Italy, including Latium, were considered
Mentions: AMOVAs were performed on 51 Heterobasidion genotypes from two H. irregulare and three H. annosum populations. Results including all loci indicated that most of the genetic variability (54–71 %) was among genotypes within population, 3–9 % of the genetic variance was among populations within species, and 25–43 % of the molecular variance was between the two species (Table 3). Averaging all loci and populations, Fst values were as high as 0.40 (SD 0.22, p-value  < 0.05). Average Fst values by each of the abovementioned categories were as follows: 0.37 for OUT loci, 0.42 for UP loci, 0.45 for IN loci, and 0.30 for DOWN loci. Details on percentage of per locus variance, as well as Fst and gene flow (2 Nm) values, calculated considering the genotypes as haploids, are summarized in Fig. 5 and Additional file 2, respectively. The genetic diversity detected with the 39 loci was sufficiently informative to reflect the genetic distinction between species. The PCoA showed a clear genetic differentiation between H. irregulare and H. annosum, especially when UP and IN loci were considered (Fig. 6). In IN loci no overlap between species was observed, while in OUT, UP, and DOWN loci partial overlap was observed between H. irregulare genotypes and H. annosum genotypes from the Latium population (LZO-AN) (Fig. 6).Table 3

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