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The Expansion of Animal MicroRNA Families Revisited

by 1 and 1,2,3,4,5,6,7,*
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103 Leipzig, Germany
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany
Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
Author to whom correspondence should be addressed.
Academic Editor: Pabulo H. Rampelotto
Life 2015, 5(1), 905-920;
Received: 28 November 2014 / Revised: 9 February 2015 / Accepted: 11 February 2015 / Published: 13 March 2015
(This article belongs to the Section Origin of Life)
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
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MDPI and ACS Style

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

AMA Style

Hertel J, Stadler PF. The Expansion of Animal MicroRNA Families Revisited. Life. 2015; 5(1):905-920.

Chicago/Turabian Style

Hertel, Jana, and Peter F. Stadler. 2015. "The Expansion of Animal MicroRNA Families Revisited" Life 5, no. 1: 905-920.

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