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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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Rapid evolution of a miRNA cluster. (A) The mir-64 cluster expanded by ancient and recent tandem duplications (supplementary fig. S8, Supplementary Material online). The number of mir-64 paralogs differs between C. remanei and C. latens because of the possible loss of mir-64c-1 in C. remanei. (B) Genetic differentiation of mir-64 members among three populations of C. remanei. mir-64c is highly differentiated between samples from Ohio and Ontario, suggesting that mir-64c may be the target of adaptive evolution. The dash line represents the 95 percentile of FST values in a set of protein-coding genes. (C) Distance matrices between paralogs and orthologs in C. remanei and C. latens for the entire hairpin sequence (below diagonal) and for the mature sequence (above diagonal). Crem, C. remanei; Cla, C. latens.
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evu239-F7: Rapid evolution of a miRNA cluster. (A) The mir-64 cluster expanded by ancient and recent tandem duplications (supplementary fig. S8, Supplementary Material online). The number of mir-64 paralogs differs between C. remanei and C. latens because of the possible loss of mir-64c-1 in C. remanei. (B) Genetic differentiation of mir-64 members among three populations of C. remanei. mir-64c is highly differentiated between samples from Ohio and Ontario, suggesting that mir-64c may be the target of adaptive evolution. The dash line represents the 95 percentile of FST values in a set of protein-coding genes. (C) Distance matrices between paralogs and orthologs in C. remanei and C. latens for the entire hairpin sequence (below diagonal) and for the mature sequence (above diagonal). Crem, C. remanei; Cla, C. latens.

Mentions: miRNAs are often organized along the genome in clusters that may be transcribed as a polycistronic unit (Baskerville and Bartel 2005; Axtell et al. 2011). Clustered miRNAs can experience rapid evolution in terms of species-specific tandem duplications, losses, and single nucleotide substitutions in the seed motif of homologs, as seen among species in Drosophila (Mohammed et al. 2013) and in Caenorhabditis (de Wit et al. 2009; Jovelin and Cutter 2011; Jovelin 2013; Shi et al. 2013). We found that evolution of the mir-64 cluster is particularly dynamic. Seven miRNA genes comprise this cluster in C. remanei, but C. latens contains an eighth miRNA owing to recent tandem duplication of mir-64c (fig. 7A). Phylogenetic analysis suggests that the duplication of mir-64c predates speciation between C. remanei and C. latens and that mir-64c-1 was subsequently lost in C. remanei (fig. 7A), although it remains possible that mir-64c duplicated more recently in the lineage leading to C. latens (fig. 7A and supplementary fig. S9, Supplementary Material online). We detected mir-64c-1 in all 7 strains of C. latens isolated from China and in none of the 43 strains of C. remanei from North America, Europe, and Japan, implicating the presence versus absence of mir-64c-1 as a fixed difference between these species.Fig. 7.—


Microevolution of nematode miRNAs reveals diverse modes of selection.

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

Rapid evolution of a miRNA cluster. (A) The mir-64 cluster expanded by ancient and recent tandem duplications (supplementary fig. S8, Supplementary Material online). The number of mir-64 paralogs differs between C. remanei and C. latens because of the possible loss of mir-64c-1 in C. remanei. (B) Genetic differentiation of mir-64 members among three populations of C. remanei. mir-64c is highly differentiated between samples from Ohio and Ontario, suggesting that mir-64c may be the target of adaptive evolution. The dash line represents the 95 percentile of FST values in a set of protein-coding genes. (C) Distance matrices between paralogs and orthologs in C. remanei and C. latens for the entire hairpin sequence (below diagonal) and for the mature sequence (above diagonal). Crem, C. remanei; Cla, C. latens.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu239-F7: Rapid evolution of a miRNA cluster. (A) The mir-64 cluster expanded by ancient and recent tandem duplications (supplementary fig. S8, Supplementary Material online). The number of mir-64 paralogs differs between C. remanei and C. latens because of the possible loss of mir-64c-1 in C. remanei. (B) Genetic differentiation of mir-64 members among three populations of C. remanei. mir-64c is highly differentiated between samples from Ohio and Ontario, suggesting that mir-64c may be the target of adaptive evolution. The dash line represents the 95 percentile of FST values in a set of protein-coding genes. (C) Distance matrices between paralogs and orthologs in C. remanei and C. latens for the entire hairpin sequence (below diagonal) and for the mature sequence (above diagonal). Crem, C. remanei; Cla, C. latens.
Mentions: miRNAs are often organized along the genome in clusters that may be transcribed as a polycistronic unit (Baskerville and Bartel 2005; Axtell et al. 2011). Clustered miRNAs can experience rapid evolution in terms of species-specific tandem duplications, losses, and single nucleotide substitutions in the seed motif of homologs, as seen among species in Drosophila (Mohammed et al. 2013) and in Caenorhabditis (de Wit et al. 2009; Jovelin and Cutter 2011; Jovelin 2013; Shi et al. 2013). We found that evolution of the mir-64 cluster is particularly dynamic. Seven miRNA genes comprise this cluster in C. remanei, but C. latens contains an eighth miRNA owing to recent tandem duplication of mir-64c (fig. 7A). Phylogenetic analysis suggests that the duplication of mir-64c predates speciation between C. remanei and C. latens and that mir-64c-1 was subsequently lost in C. remanei (fig. 7A), although it remains possible that mir-64c duplicated more recently in the lineage leading to C. latens (fig. 7A and supplementary fig. S9, Supplementary Material online). We detected mir-64c-1 in all 7 strains of C. latens isolated from China and in none of the 43 strains of C. remanei from North America, Europe, and Japan, implicating the presence versus absence of mir-64c-1 as a fixed difference between these species.Fig. 7.—

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