Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique.

PloS One
Hong XuJianbo Wang

Abstract

Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying embryogenesis. Here we report the transcriptome profiling analysis of rice developing embryos using RNA-Seq as an attempt to gain insight into the molecular and cellular events associated with rice embryogenesis. RNA-Seq analysis generated 17,755,890 sequence reads aligned with 27,190 genes, which provided abundant data for the analysis of rice embryogenesis. A total of 23,971, 23,732, and 23,592 genes were identified from embryos at three developmental stages (3-5, 7, and 14 DAP), while an analysis between stages allowed the identification of a subset of stage-specific genes. The number of genes expressed stage-specifically was 1,131, 1,443, and 1,223, respectively. In addition, we investigated transcriptomic changes during rice embryogenesis based on our RNA-Seq data. A total of 1,011 differentially expressed genes (DEGs) (log(2)Ratio ≥ 1, FDR ≤ 0.001) were identified; thus, the transcriptome of the developing rice embryos changed considerably. A total of 672 genes with significant changes in expression were detected between 3-5 and 7 DAP; 504 DEGs were identified between 7 and 14 DAP. A large number of genes related to metabolism, tra...Continue Reading

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Citations

Dec 12, 2012·International Journal of Plant Genomics·Santosh KumarSylvie Cloutier
Jan 25, 2014·BMC Genomics·Wenqin WangJoachim Messing
Jun 4, 2013·Trends in Plant Science·Joakim PalovaaraDolf Weijers
Jan 17, 2013·Plant Molecular Biology·Yi GaoJianbo Wang
May 6, 2015·Journal of Experimental Botany·Naoto SanoMotoki Kanekatsu
Nov 29, 2012·PloS One·Wenlan LiJianbo Wang
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Dec 31, 2018·BMC Plant Biology·Andreia S RodriguesCélia M Miguel
Jul 25, 2019·Scientific Reports·Liziane Cristina Campos Brusamarello-SantosEmanuel Maltempi de Souza
Oct 18, 2020·International Journal of Molecular Sciences·Shuo SunHuixia Shou
Apr 4, 2021·Microorganisms·Mohamad Syazwan NgalimatMohd Termizi Yusof

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Methods Mentioned

BETA
transcription profiling
RNA-Seq
dissection
Assay
Chip

Software Mentioned

Blast2GO
soap2
SOAPaligner
R package DEGseq
Cytoscape
ERANGE

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