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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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miRNAs from families unique to C. remanei are expressed at lower levels than miRNAs from families conserved in other Caenorhabditis species. Expression read counts from de Wit et al. (2009).
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evu239-F6: miRNAs from families unique to C. remanei are expressed at lower levels than miRNAs from families conserved in other Caenorhabditis species. Expression read counts from de Wit et al. (2009).

Mentions: The evolution of novel miRNAs could have genome-wide consequences on gene regulation owing to the small motifs of sequence complementarity required for binding to potential targets (Bartel 2009; Zheng et al. 2011). However, low and/or restricted spatio-temporal expression of newly emerging miRNAs could limit the deleterious effects of novel regulatory interactions (Chen and Rajewsky 2007). Consistent with this hypothesis, we found that phylogenetically restricted miRNAs have significantly lower expression in C. remanei (fig. 6). In addition, miRNA expression level in C. remanei correlates negatively with the amount of nucleotide variability (hairpin: Spearman’s ρ = −0.214, P = 0.017; backbone: ρ = −0.207, P = 0.021; miR: ρ −0.221, P = 0.014). A qualitatively similar, nonsignificant trend involving miRNA expression level is present for sequence divergence between orthologs in C. remanei and C. latens (hairpin: ρ = −0.184, P = 0.110; backbone: ρ = −0.186, P = 0.106; miR: ρ = −0.206, P = 0.072). These results suggest that low expression of novel miRNA genes could delay their elimination and may enable their integration into regulatory networks while also allowing faster sequence evolution, perhaps facilitated by positive selection (Lyu et al. 2014).Fig. 6.—


Microevolution of nematode miRNAs reveals diverse modes of selection.

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

miRNAs from families unique to C. remanei are expressed at lower levels than miRNAs from families conserved in other Caenorhabditis species. Expression read counts from de Wit et al. (2009).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu239-F6: miRNAs from families unique to C. remanei are expressed at lower levels than miRNAs from families conserved in other Caenorhabditis species. Expression read counts from de Wit et al. (2009).
Mentions: The evolution of novel miRNAs could have genome-wide consequences on gene regulation owing to the small motifs of sequence complementarity required for binding to potential targets (Bartel 2009; Zheng et al. 2011). However, low and/or restricted spatio-temporal expression of newly emerging miRNAs could limit the deleterious effects of novel regulatory interactions (Chen and Rajewsky 2007). Consistent with this hypothesis, we found that phylogenetically restricted miRNAs have significantly lower expression in C. remanei (fig. 6). In addition, miRNA expression level in C. remanei correlates negatively with the amount of nucleotide variability (hairpin: Spearman’s ρ = −0.214, P = 0.017; backbone: ρ = −0.207, P = 0.021; miR: ρ −0.221, P = 0.014). A qualitatively similar, nonsignificant trend involving miRNA expression level is present for sequence divergence between orthologs in C. remanei and C. latens (hairpin: ρ = −0.184, P = 0.110; backbone: ρ = −0.186, P = 0.106; miR: ρ = −0.206, P = 0.072). These results suggest that low expression of novel miRNA genes could delay their elimination and may enable their integration into regulatory networks while also allowing faster sequence evolution, perhaps facilitated by positive selection (Lyu et al. 2014).Fig. 6.—

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