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Life 2015, 5(1), 905-920; doi:10.3390/life5010905

The Expansion of Animal MicroRNA Families Revisited

1
and
1,2,3,4,5,6,7,*
1
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany
2
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103 Leipzig, Germany
3
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
4
Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany
5
Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
6
Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
7
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Pabulo H. Rampelotto
Received: 28 November 2014 / Revised: 9 February 2015 / Accepted: 11 February 2015 / Published: 13 March 2015
(This article belongs to the Section Chemistry)
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Abstract

MicroRNAs are important regulatory small RNAs in many eukaryotes. Due to their small size and simple structure, they are readily innovated de novo. Throughout the evolution of animals, the emergence of novel microRNA families traces key morphological innovations. Here, we use a computational approach based on homology search and parsimony-based presence/absence analysis to draw a comprehensive picture of microRNA evolution in 159 animal species. We confirm previous observations regarding bursts of innovations accompanying the three rounds of genome duplications in vertebrate evolution and in the early evolution of placental mammals. With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea. More importantly, we see clear evidence that loss of microRNA families is not an uncommon phenomenon. The Enoplea may serve as a second dramatic example beyond the tunicates. The large-scale analysis presented here also highlights several generic technical issues in the analysis of very large gene families that will require further research. View Full-Text
Keywords: microRNA; gene loss; genome duplication; innovation; Dollo parsimony; Metazoa microRNA; gene loss; genome duplication; innovation; Dollo parsimony; Metazoa
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Hertel, J.; Stadler, P.F. The Expansion of Animal MicroRNA Families Revisited. Life 2015, 5, 905-920.

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