PUBLICATION

Evolution after whole genome duplication: teleost microRNAs

Authors
Desvignes, T., Sydes, J., Montfort, J., Bobe, J., Postlethwait, J.H.
ID
ZDB-PUB-210420-14
Date
2021
Source
Molecular Biology and Evolution   38(8): 3308-3331 (Journal)
Registered Authors
Bobe, Julien, Desvignes, Thomas, Postlethwait, John H.
Keywords
Blackfin icefish Chaenocephalus aceratus, Japanese medaka Oryzias latipes, Spotted gar Lepisosteus oculatus, Three-spined stickleback Gasterosteus aculeatus, arm-switching, zebrafish Danio rerio
MeSH Terms
  • Animals
  • Base Sequence
  • Biological Evolution*
  • Conserved Sequence
  • Fishes/genetics*
  • Fishes/metabolism
  • Gene Duplication
  • Genome*
  • Gonads/metabolism
  • MicroRNAs/genetics*
  • Multigene Family
  • Selection, Genetic
  • Species Specificity
PubMed
33871629 Full text @ Mol Bio Evol
Abstract
microRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the Teleost Genome Duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than non-clustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3' complementary regions, compared to minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multi-species analysis of the mechanisms influencing metazoan miRNA evolution after whole genome duplication.
Genes / Markers
Figures
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Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping