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Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species.

Behura SK, Severson DW - DNA Res. (2014)

Bottom Line: The results show that varying proportions (∼15-46%) of microsatellites identified in these species are imperfect in motif structure, and that they also vary in chromosomal distribution within genomes.It was observed that the genomic abundance of imperfect repeats is significantly associated with the length and number of motif mismatches of microsatellites.Using Drosophila Reference Genetic Panel data, we further show that pattern of allelic variation modulates motif heterogeneity of microsatellites, and provide estimates of allele age of specific imperfect microsatellites found within protein-coding genes.

View Article: PubMed Central - PubMed

Affiliation: Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA sbehura@nd.edu.

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Distribution of likelihoods of allele age (generations ago) of the mutation (SNP) in the microsatellite sequences. The SNP IDs along with their alleles are shown above the graphs. The x-axis represents time (in generations) when the mutation likely occurred, and the corresponding estimates of likelihoods are shown in the y-axis. The specific generation time when the likelihood value is highest is indicated by an upward arrow.
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DSU036F6: Distribution of likelihoods of allele age (generations ago) of the mutation (SNP) in the microsatellite sequences. The SNP IDs along with their alleles are shown above the graphs. The x-axis represents time (in generations) when the mutation likely occurred, and the corresponding estimates of likelihoods are shown in the y-axis. The specific generation time when the likelihood value is highest is indicated by an upward arrow.

Mentions: We also estimated the age of specific alleles of imperfect microsatellites based on the population data (DGRP). First, we identified flanking mutations (within 1 kb on both ends) of microsatellites that were in complete linkage with segregating mutation within the microsatellite (Supplementary Fig. S1). Based on the results of phylogenetic analysis, the extended sequences showed differential genealogical relations among the inbred lines (Fig. 5). We determined the number of fixed mutations, total number of variable sites and the average number of nucleotide differences in the extended sequences of imperfect microsatellites (Supplementary Table S8). Based on the allele frequency of mutations within and the flanking sequences of the imperfect microsatellite, we predicted generation times that might have lapsed since the origin of the mutation in the microsatellite. The maximum likelihood method17 was used for making this prediction from the joint distribution of the number of copies in the population and the coalescence times of the intra-allelic variation. The results revealed that the maximum likelihoods varied between 1,380 and 1,530 generations (Fig. 6). Assuming 36 days as the average generation time of D. melanogaster, it was thus estimated that these alleles might have arisen 136–150 yrs ago.Figure 5.


Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species.

Behura SK, Severson DW - DNA Res. (2014)

Distribution of likelihoods of allele age (generations ago) of the mutation (SNP) in the microsatellite sequences. The SNP IDs along with their alleles are shown above the graphs. The x-axis represents time (in generations) when the mutation likely occurred, and the corresponding estimates of likelihoods are shown in the y-axis. The specific generation time when the likelihood value is highest is indicated by an upward arrow.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379975&req=5

DSU036F6: Distribution of likelihoods of allele age (generations ago) of the mutation (SNP) in the microsatellite sequences. The SNP IDs along with their alleles are shown above the graphs. The x-axis represents time (in generations) when the mutation likely occurred, and the corresponding estimates of likelihoods are shown in the y-axis. The specific generation time when the likelihood value is highest is indicated by an upward arrow.
Mentions: We also estimated the age of specific alleles of imperfect microsatellites based on the population data (DGRP). First, we identified flanking mutations (within 1 kb on both ends) of microsatellites that were in complete linkage with segregating mutation within the microsatellite (Supplementary Fig. S1). Based on the results of phylogenetic analysis, the extended sequences showed differential genealogical relations among the inbred lines (Fig. 5). We determined the number of fixed mutations, total number of variable sites and the average number of nucleotide differences in the extended sequences of imperfect microsatellites (Supplementary Table S8). Based on the allele frequency of mutations within and the flanking sequences of the imperfect microsatellite, we predicted generation times that might have lapsed since the origin of the mutation in the microsatellite. The maximum likelihood method17 was used for making this prediction from the joint distribution of the number of copies in the population and the coalescence times of the intra-allelic variation. The results revealed that the maximum likelihoods varied between 1,380 and 1,530 generations (Fig. 6). Assuming 36 days as the average generation time of D. melanogaster, it was thus estimated that these alleles might have arisen 136–150 yrs ago.Figure 5.

Bottom Line: The results show that varying proportions (∼15-46%) of microsatellites identified in these species are imperfect in motif structure, and that they also vary in chromosomal distribution within genomes.It was observed that the genomic abundance of imperfect repeats is significantly associated with the length and number of motif mismatches of microsatellites.Using Drosophila Reference Genetic Panel data, we further show that pattern of allelic variation modulates motif heterogeneity of microsatellites, and provide estimates of allele age of specific imperfect microsatellites found within protein-coding genes.

View Article: PubMed Central - PubMed

Affiliation: Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA sbehura@nd.edu.

Show MeSH
Related in: MedlinePlus