Summary: 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.
Overall Design: 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.
Treatment Protocol:
-
Extract Protocol:
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).
Library Construction Protocol:
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).
Sequencing
Molecule Type:
poly(A)+ RNA
Library Source:
Library Layout:
SINGLE
Library Strand:
-
Platform:
ILLUMINA
Instrument Model:
Illumina Genome Analyzer IIx
Strand-Specific:
Unspecific
Samples
Basic Information:
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Biological Condition:
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Sequencing:
Assessing Quality:
Analysis:
Data Resource
GEN Sample ID
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Species
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Tissue
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Mutation
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Case Detail
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Extract Protocol
Library Construction Protocol
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Strand-Specific
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Gbases
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AvgSpotLen2
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Publications
Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.
Genome biology and evolution . 2011-10-31 [PMID:
22042334]
