title: Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species.
abstract: BACKGROUND
  Understanding how species-specific microRNAs (miRNAs) contribute to species-specific phenotypes is a central topic in biology. This study aimed to elucidate the role of ruminant-specific miRNAs in shaping mRNA expression divergence between ruminant and non-ruminant species.
  
  
  RESULTS
  We analyzed miRNA and mRNA transcriptomes generated by Illumina sequencing from whole blood samples of cattle and a closely related non-ruminant species, pig. We found evidence of expansion of cattle-specific miRNAs by analyzing miRNA conservation among 57 vertebrate species. The emergence of cattle-specific miRNAs was accompanied by accelerated sequence evolution at their target sites. Further, the target genes of cattle-specific miRNAs show markedly reduced expression compared to their pig and human orthologues. We found that target genes with conserved or non-conserved target sites of cattle-specific miRNAs exhibit reduced expression. One of the significantly enriched KEGG pathway terms for the target genes of the cattle-specific miRNAs is the insulin signalling pathway, raising the possibility that some of these miRNAs may modulate insulin resistance in ruminants.
  
  
  CONCLUSIONS
  We provide evidence of rapid miRNA-mediated regulatory evolution in the ruminant lineage. Cattle-specific miRNAs play an important role in shaping gene expression divergence between ruminant and non-ruminant species, by influencing the expression of targets genes through both conserved and cattle-specific target sites.
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada. lguan@ualberta.ca.
authors.forename: Hua
authors.initials: H
authors.lastname: Bao
authors.forename: Arun
authors.initials: A
authors.lastname: Kommadath
authors.forename: Xu
authors.initials: X
authors.lastname: Sun
authors.forename: Yan
authors.initials: Y
authors.lastname: Meng
authors.forename: Adriano S
authors.initials: AS
authors.lastname: Arantes
authors.forename: Graham S
authors.initials: GS
authors.lastname: Plastow
authors.forename: Le Luo
authors.initials: LL
authors.lastname: Guan
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle / Q000235:genetics*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D015723:Gene Library; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D012418:Ruminants / Q000235:genetics*; D013045:Species Specificity; D013552:Swine; D059467:Transcriptome
chemical_list: D035683:MicroRNAs
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