概要: 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.
项目整体设计: In order to investigate expression patterns of rice retrogenes, the transcriptome of seven tissues, callus, leaf, panicle before flowering, pannicle after flowering, root, seed, and shoot, was sequenced by Illumina sequencing (RNA-seq).
The seeds were germinated in a growth chamber at 28 °C under a 16-h light/8-h dark regime. Seven days after germination, shoots and roots were collected. In the meantime, plants were grown in paddy fields, where leaves (7 days before heading to 7 days after flowering) and panicles (7 days before and 0–7 days after heading to flowering) were collected. Callus was induced on N6D medium according to a previous protocol.
处理方案:
-
提取方案:
Total RNA was extracted from each tissue with the RNeasy Plant mini kit (Qiagen), and cDNA was synthesized with mRNAseq 8-sample prep kit (Illumina) (Mizuno et al. 2010).
建库方案:
We constructed cDNA libraries for the seven tissues individually and sequenced single ends of each on the Illumina GAIIx platform for four separate runs (three at 36 cycles and one at 76 cycles).
测序信息
分子类型:
poly(A)+ RNA
库的片段类型:
SINGLE
库的链类型:
-
测序平台:
ILLUMINA
测序仪型号:
Illumina Genome Analyzer IIx
链特异性:
Unspecific
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文章
Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.
Genome biology and evolution . 2011-10-31 [PMID:
22042334]
