RRC ID 57444
Author Kenny NJ, Sin YW, Hayward A, Paps J, Chu KH, Hui JH.
Title The phylogenetic utility and functional constraint of microRNA flanking sequences.
Journal Proc. Biol. Sci.
Abstract MicroRNAs (miRNAs) have recently risen to prominence as novel factors responsible for post-transcriptional regulation of gene expression. miRNA genes have been posited as highly conserved in the clades in which they exist. Consequently, miRNAs have been used as rare genome change characters to estimate phylogeny by tracking their gain and loss. However, their short length (21-23 bp) has limited their perceived utility in sequenced-based phylogenetic inference. Here, using reference taxa with established phylogenetic relationships, we demonstrate that miRNA sequences are of high utility in quantitative, rather than in qualitative, phylogenetic analysis. The clear orthology among miRNA genes from different species makes it straightforward to identify and align these sequences from even fragmentary datasets. We also identify significant sequence conservation in the regions directly flanking miRNA genes, and show that this too is of utility in phylogenetic analysis, as well as highlighting conserved regions that will be of interest to other fields. Employing miRNA sequences from 12 sequenced drosophilid genomes, together with a Tribolium castaneum outgroup, we demonstrate that this approach is robust using Bayesian and maximum-likelihood methods. The utility of these characters is further demonstrated in the rhabditid nematodes and primates. As next-generation sequencing makes it more cost-effective to sequence genomes and small RNA libraries, this methodology provides an alternative data source for phylogenetic analysis. The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.
Volume 282(1803)
Pages 20142983
Published 2015-3-22
DOI 10.1098/rspb.2014.2983
PII rspb.2014.2983
PMID 25694624
PMC PMC4345462
MeSH Animals Base Sequence Bayes Theorem Conserved Sequence Drosophilidae / genetics Evolution, Molecular Likelihood Functions MicroRNAs / genetics* Molecular Sequence Data Phylogeny Sequence Analysis, RNA Species Specificity Tribolium / genetics
IF 4.304