Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique.
Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique.
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DOI：
10.1371/journal.pone.0030646
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Xu H;Gao Y;Wang J
水稻（Oryza sativa）是一种具有已知基因组序列的优秀单子叶植物，可用于胚胎发生研究。在这里，我们报告了利用RNA-Seq对水稻发育胚胎的转录组分析，试图深入了解与水稻胚胎发生相关的分子和细胞事件。RNA-Seq分析得到17755890个序列，与27190个基因对齐，为水稻胚胎发生分析提供了丰富的数据。在三个发育阶段（3 - 5,7和14 DAP）的胚胎中共鉴定出23,971,23,732和23,592个基因，而阶段之间的分析允许鉴定出阶段特异性基因的子集。阶段特异性表达的基因数量分别为1,131,1,443和1,223。此外，我们基于RNA-Seq数据研究了水稻胚胎发生过程中的转录组学变化。共鉴定出1011个差异表达基因（DEGs） （log2Ratio≥1,FDR≤0.001）；因此，发育中的水稻胚胎的转录组发生了很大的变化。在3-5 ~ 7 DAP之间共检测到672个表达显著变化的基因；在7 ~ 14 DAP之间鉴定出504个deg。大量与代谢、转录调控、核酸复制/加工和信号转导相关的基因在胚胎发生的早期和中期主要表达。蛋白质生物合成相关基因主要在胚胎中期积累。淀粉/蔗糖代谢和蛋白质修饰基因在胚胎发生中后期高度表达。此外，我们发现许多转录因子家族可能在不同的发育阶段发挥重要作用，不仅在胚胎起始，而且在其他发育过程中。这些结果将扩大我们对水稻胚胎发生过程中复杂的分子和细胞事件的认识，并为进一步研究水稻和其他谷类作物的胚胎发育奠定基础。
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) (log2Ratio ≥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, transcriptional regulation, nucleic acid replication/processing, and signal transduction were expressed predominantly in the early and middle stages of embryogenesis. Protein biosynthesis-related genes accumulated predominantly in embryos at the middle stage. Genes for starch/sucrose metabolism and protein modification were highly expressed in the middle and late stages of embryogenesis. In addition, we found that many transcription factor families may play important roles at different developmental stages, not only in embryo initiation but also in other developmental processes. These results will expand our understanding of the complex molecular and cellular events in rice embryogenesis and provide a foundation for future studies on embryo development in rice and other cereal crops.
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影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
7.2
作者：
Colombo, Monica;Masiero, Simona;Colombo, Lucia
通讯作者：
Colombo, Lucia
DOI：
10.1093/bioinformatics/btp101
发表时间：
2009-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bindea G;Mlecnik B;Hackl H;Charoentong P;Tosolini M;Kirilovsky A;Fridman WH;Pagès F;Trajanoski Z;Galon J
通讯作者：
Galon J
DEGseq：一个 R 包，用于从 RNA-seq 数据中识别差异表达基因
影响因子：
5.8
作者：
Wang, Likun;Feng, Zhixing;Zhang, Xuegong
通讯作者：
Zhang, Xuegong
影响因子：
4.6
作者：
Chandler, John W.;Cole, Melanie;Werr, Wolfgang
通讯作者：
Werr, Wolfgang