Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi

BMC Genomics

Research Article

Patrick Lemaire¹  Christelle Dantec¹  Takeshi A. Onuma²  Hiroki Nishida²  Kai Wang³ 

[1] Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France;Department of Biological Sciences, Graduate School of Science, Osaka University, 560-0043, Toyonaka, Osaka, Japan;Department of Biological Sciences, Graduate School of Science, Osaka University, 560-0043, Toyonaka, Osaka, Japan;Present address: Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Science, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, People’s Republic of China;

关键词: Ascidian;    Halocynthia roretzi;    miRNA;    Genome-wide survey;    miRNA targets;   

DOI  :  10.1186/s12864-017-3707-5

 received in 2016-12-05, accepted in 2017-04-12,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundmiRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied.ResultsWe report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans.ConclusionOur study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones.

【 授权许可】

CC BY   
© The Author(s). 2017