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

Xu H, Gao Y, Wang J - PLoS ONE (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.

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, 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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Changes in gene expression profile among the different developmental stages.The number of up-regulated and down-regulated genes between R1 and R2, R2 and R3 are summarized. Between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, there are 275 genes up-regulated and 397 genes down-regulated, while there are 128 up-regulated genes and 376 down-regulated genes between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries.
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pone-0030646-g004: Changes in gene expression profile among the different developmental stages.The number of up-regulated and down-regulated genes between R1 and R2, R2 and R3 are summarized. Between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, there are 275 genes up-regulated and 397 genes down-regulated, while there are 128 up-regulated genes and 376 down-regulated genes between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries.

Mentions: To identify genes showing a significant change in expression during different developmental stages, the differentially expressed tags between two samples were identified using an algorithm developed by Audic et al.[24]. A total of 672 significantly changed genes were detected between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, with 275 genes up-regulated and 397 genes down-regulated (Figure 4 and Table S2). Between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries, a total of 504 DEGs were detected, with 128 up-regulated genes and 376 down-regulated genes (Figure 4 and Table S3). This suggests that the differentiation of expressed genes between R1 (3 DAP) and R2 (7 DAP) is larger than that between R2 (7 DAP) and R3 (14 DAP).


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

Xu H, Gao Y, Wang J - PLoS ONE (2012)

Changes in gene expression profile among the different developmental stages.The number of up-regulated and down-regulated genes between R1 and R2, R2 and R3 are summarized. Between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, there are 275 genes up-regulated and 397 genes down-regulated, while there are 128 up-regulated genes and 376 down-regulated genes between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3275597&req=5

pone-0030646-g004: Changes in gene expression profile among the different developmental stages.The number of up-regulated and down-regulated genes between R1 and R2, R2 and R3 are summarized. Between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, there are 275 genes up-regulated and 397 genes down-regulated, while there are 128 up-regulated genes and 376 down-regulated genes between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries.
Mentions: To identify genes showing a significant change in expression during different developmental stages, the differentially expressed tags between two samples were identified using an algorithm developed by Audic et al.[24]. A total of 672 significantly changed genes were detected between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, with 275 genes up-regulated and 397 genes down-regulated (Figure 4 and Table S2). Between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries, a total of 504 DEGs were detected, with 128 up-regulated genes and 376 down-regulated genes (Figure 4 and Table S3). This suggests that the differentiation of expressed genes between R1 (3 DAP) and R2 (7 DAP) is larger than that between R2 (7 DAP) and R3 (14 DAP).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.

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, 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.

Show MeSH