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Open Access Short Report

Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features

Ming Zou12, Guoxiu Wang3 and Shunping He1*

Author Affiliations

1 The key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China

2 University of the Chinese Academy of Sciences, Beijing 100039, PR China

3 Hubei Key Laboratory of Genetic Regulation and Integrative Biology, HuaZhong Normal University, Wuhan, Hubei, China

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BMC Research Notes 2012, 5:398  doi:10.1186/1756-0500-5-398

Published: 1 August 2012

Abstract

Background

RNA-based gene duplicates (retrocopies) played pivotal roles in many physiological processes. Nowadays, functional retrocopies have been systematically identified in several mammals, fruit flies, plants, zebrafish and other chordates, etc. However, studies about this kind of duplication in Caenorhabditis nematodes have not been reported.

Findings

We identified 43, 48, 43, 9, and 42 retrocopies, of which 6, 15, 18, 3, and 13 formed chimeric genes in C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. At least 5 chimeric types exist in Caenorhabditis species, of which retrocopy recruiting both N and C terminus is the commonest one. Evidences from different analyses demonstrate many retrocopies and almost all chimeric genes may be functional in these species. About half of retrocopies in each species has coordinates in other species, and we suggest that retrocopies in closely related species may be helpful in identifying retrocopies for one certain species.

Conclusions

A number of retrocopies and chimeric genes exist in Caenorhabditis genomes, and some of them may be functional. The evolutionary patterns of these genes may correlate with their genomic features, such as the activity of retroelements, the high rate of mutation and deletion rate, and a large proportion of genes subject to trans-splicing.

Keywords:
Retrocopy; Chimeric gene; Caenorhabditis; Evolutionary pattern