The Expansion of Animal MicroRNA Families Revisited

Life

Jana Hertel¹  Peter F. Stadler¹ 

[1] Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany; E-Mail:

关键词: microRNA;    gene loss;    genome duplication;    innovation;    Dollo parsimony;    Metazoa;   

DOI  :  10.3390/life5010905

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.