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Microevolution of nematode miRNAs reveals diverse modes of selection.

Jovelin R, Cutter AD - Genome Biol Evol (2014)

Bottom Line: We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence.Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species.These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada richard.jovelin@utoronto.ca.

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The level of selective constraints varies among different regions of the miRNA hairpin. (A) Diagram of a stereotypical miRNA hairpin with a stem-loop structure. The number of mutations segregating in the population from Ohio and the number of substitutions between Caenorhabditis remanei and Caenorhabditis latens are respectively shown in parentheses for each region of the miRNA (i.e., polymorphisms: substitutions). (B) Nucleotide differences in miRNA regions are lower than nucleotide differences at synonymous sites of protein-coding genes. Light blue, within species variation; dark blue, between species divergence; miR, mature miRNA; miR*, star sequence. Means are represented ± 1 standard error of the mean.
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evu239-F1: The level of selective constraints varies among different regions of the miRNA hairpin. (A) Diagram of a stereotypical miRNA hairpin with a stem-loop structure. The number of mutations segregating in the population from Ohio and the number of substitutions between Caenorhabditis remanei and Caenorhabditis latens are respectively shown in parentheses for each region of the miRNA (i.e., polymorphisms: substitutions). (B) Nucleotide differences in miRNA regions are lower than nucleotide differences at synonymous sites of protein-coding genes. Light blue, within species variation; dark blue, between species divergence; miR, mature miRNA; miR*, star sequence. Means are represented ± 1 standard error of the mean.

Mentions: We discovered a total of 381 SNPs and 32 indels located within 129 miRNA gene hairpins in an Ohio population of C. remanei (fig. 1A and supplementary table S1, Supplementary Material online). This gene collection comprises a large majority of the miRNAs in the genome: 83% of miRNAs identified in de Wit et al. (2009) and 69% of miRBase release 20 miRNAs (Kozomara and Griffiths-Jones 2011) that include a recent update of Caenorhabditis miRNAs (Shi et al. 2013). Nearly one-third (29%) of miRNA hairpins had no polymorphisms at all, although polymorphic miRNAs contained up to 20 variable sites. Subsequent analysis of C. remanei strains from Germany and Ontario revealed respectively 153 and 151 SNPs and 11 and 10 indels in a subset of 38 miRNA genes that we had found to have allelic variation within Ohio (supplementary table S1, Supplementary Material online). And, for the 79 miRNAs that we sequenced in the closely related species C. latens, we identified 302 nt substitutions and 37 indel differences between the 2 species. This wealth and density of mutations in miRNA genes within a single species and between sister species thus provide a powerful substrate to test the processes driving their microevolutionary dynamics.Fig. 1.—


Microevolution of nematode miRNAs reveals diverse modes of selection.

Jovelin R, Cutter AD - Genome Biol Evol (2014)

The level of selective constraints varies among different regions of the miRNA hairpin. (A) Diagram of a stereotypical miRNA hairpin with a stem-loop structure. The number of mutations segregating in the population from Ohio and the number of substitutions between Caenorhabditis remanei and Caenorhabditis latens are respectively shown in parentheses for each region of the miRNA (i.e., polymorphisms: substitutions). (B) Nucleotide differences in miRNA regions are lower than nucleotide differences at synonymous sites of protein-coding genes. Light blue, within species variation; dark blue, between species divergence; miR, mature miRNA; miR*, star sequence. Means are represented ± 1 standard error of the mean.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255771&req=5

evu239-F1: The level of selective constraints varies among different regions of the miRNA hairpin. (A) Diagram of a stereotypical miRNA hairpin with a stem-loop structure. The number of mutations segregating in the population from Ohio and the number of substitutions between Caenorhabditis remanei and Caenorhabditis latens are respectively shown in parentheses for each region of the miRNA (i.e., polymorphisms: substitutions). (B) Nucleotide differences in miRNA regions are lower than nucleotide differences at synonymous sites of protein-coding genes. Light blue, within species variation; dark blue, between species divergence; miR, mature miRNA; miR*, star sequence. Means are represented ± 1 standard error of the mean.
Mentions: We discovered a total of 381 SNPs and 32 indels located within 129 miRNA gene hairpins in an Ohio population of C. remanei (fig. 1A and supplementary table S1, Supplementary Material online). This gene collection comprises a large majority of the miRNAs in the genome: 83% of miRNAs identified in de Wit et al. (2009) and 69% of miRBase release 20 miRNAs (Kozomara and Griffiths-Jones 2011) that include a recent update of Caenorhabditis miRNAs (Shi et al. 2013). Nearly one-third (29%) of miRNA hairpins had no polymorphisms at all, although polymorphic miRNAs contained up to 20 variable sites. Subsequent analysis of C. remanei strains from Germany and Ontario revealed respectively 153 and 151 SNPs and 11 and 10 indels in a subset of 38 miRNA genes that we had found to have allelic variation within Ohio (supplementary table S1, Supplementary Material online). And, for the 79 miRNAs that we sequenced in the closely related species C. latens, we identified 302 nt substitutions and 37 indel differences between the 2 species. This wealth and density of mutations in miRNA genes within a single species and between sister species thus provide a powerful substrate to test the processes driving their microevolutionary dynamics.Fig. 1.—

Bottom Line: We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence.Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species.These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada richard.jovelin@utoronto.ca.

Show MeSH
Related in: MedlinePlus