Tarver, JE, Taylor, RS, Puttick, MN et al. (7 more authors) (2018) Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biology and Evolution, 10 (6). pp. 1457-1470. ISSN 1759-6653
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 of microRNAs 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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | (c) The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | microRNAs; annotation; evolution; birth; death; phylogeny |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Environment (Leeds) > School of Earth and Environment (Leeds) > Earth Surface Science Institute (ESSI) (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 13 Sep 2018 10:56 |
Last Modified: | 13 Sep 2018 10:56 |
Status: | Published |
Publisher: | Oxford University Press |
Identification Number: | 10.1093/gbe/evy096 |
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Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:135591 |