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Genome biology and evolution
2011;3 1357-68.

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Hiroaki Sakai, Hiroshi Mizuno, Yoshihiro Kawahara, Hironobu Wakimoto, Hiroshi Ikawa, Hiroyuki Kawahigashi, Hiroyuki Kanamori, Takashi Matsumoto, Takeshi Itoh, Brandon S Gaut
Author Information
  1. Hiroaki Sakai: Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
PMID: 22042334 DOI: 10.1093/gbe/evr111

Abstract

Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between DNA-based duplicates. In this study, we identified 150 retrocopies in rice (Oryza sativa L. ssp japonica), most of which represent ancient retroposition events. We measured their expression from high-throughput RNA sequencing (RNAseq) data generated from seven tissues. At least 66% of the retrocopies were expressed but at lower levels than their source genes. However, the tissue specificity of retrogenes was similar to their source genes, and expression between retrocopies and source genes was correlated across tissues. The level of correlation was similar between RNA- and DNA-based duplicates, and they decreased over time at statistically indistinguishable rates. We extended these observations to previously identified retrocopies in Arabidopsis thaliana, suggesting they may be general features of the process of retention of plant retrogenes.

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Grants

  1. UL1 TR000001/NCATS NIH HHS

MeSH Term

Arabidopsis
Gene Duplication
Gene Expression
Genes, Plant
High-Throughput Nucleotide Sequencing
Oryza
RNA, Plant
Retroelements
Sequence Analysis, RNA

Chemicals

RNA, Plant
Retroelements
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Links to CNCB-NGDC Resources

GEN: GEND000292 (Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes)

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