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

Overview of attention for article published in BMC Genomics, December 2015
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Title
Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system
Published in
BMC Genomics, December 2015
DOI 10.1186/s12864-015-2274-x
Pubmed ID
Authors

Paolo Gonthier, Fabiano Sillo, Elisa Lagostina, Angela Roccotelli, Olga Santa Cacciola, Jan Stenlid, Matteo Garbelotto

Abstract

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 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. 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.

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Mendeley readers

The data shown below were compiled from readership statistics for 38 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 3%
Colombia 1 3%
Unknown 36 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 24%
Student > Doctoral Student 4 11%
Professor 4 11%
Student > Bachelor 3 8%
Other 3 8%
Other 9 24%
Unknown 6 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 18 47%
Environmental Science 5 13%
Biochemistry, Genetics and Molecular Biology 2 5%
Pharmacology, Toxicology and Pharmaceutical Science 1 3%
Arts and Humanities 1 3%
Other 3 8%
Unknown 8 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 30 December 2015.
All research outputs
#10,036,616
of 15,757,191 outputs
Outputs from BMC Genomics
#5,454
of 8,809 outputs
Outputs of similar age
#198,295
of 371,579 outputs
Outputs of similar age from BMC Genomics
#739
of 1,007 outputs
Altmetric has tracked 15,757,191 research outputs across all sources so far. This one is in the 23rd percentile – i.e., 23% of other outputs scored the same or lower than it.
So far Altmetric has tracked 8,809 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 30th percentile – i.e., 30% of its peers scored the same or lower than it.
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