Well-annotated microRNAomes do not evidence pervasive miRNA loss

James E. Tarver, Richard S. Taylor, Mark N. Puttick, Graeme T. Lloyd, Walker Pett, Bastian Fromm, Bettina E. Schirrmeister, Davide Pisani, Kevin J. Peterson, Philip C.J. Donoghue

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

MicroRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility ofmicroRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes.Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92%are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.

Original languageEnglish
Pages (from-to)1457-1470
Number of pages14
JournalGenome biology and evolution
Volume10
Issue number6
DOIs
Publication statusPublished - 1 Jun 2018

Keywords

  • Annotation
  • Birth
  • Death
  • Evolution
  • MicroRNAs
  • Phylogeny

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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  • Cite this

    Tarver, J. E., Taylor, R. S., Puttick, M. N., Lloyd, G. T., Pett, W., Fromm, B., Schirrmeister, B. E., Pisani, D., Peterson, K. J., & Donoghue, P. C. J. (2018). Well-annotated microRNAomes do not evidence pervasive miRNA loss. Genome biology and evolution, 10(6), 1457-1470. https://doi.org/10.1093/gbe/evy096