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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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Histogram presentation of gene ontology (GO) classification.The results are summarized in three main categories: biological process, molecular function and cellular component. The y-axis indicates the number of genes in a category. In three main categories of GO classification, there are 16, 17, and 20 functional groups, respectively. Metabolic process (GO: 0008152), with 851 genes, are dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, are dominant in the main categories of molecular function and cellular component, respectively.
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pone-0030646-g003: Histogram presentation of gene ontology (GO) classification.The results are summarized in three main categories: biological process, molecular function and cellular component. The y-axis indicates the number of genes in a category. In three main categories of GO classification, there are 16, 17, and 20 functional groups, respectively. Metabolic process (GO: 0008152), with 851 genes, are dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, are dominant in the main categories of molecular function and cellular component, respectively.

Mentions: To facilitate the global analysis of gene expression, all predicted rice genes were assigned to different functional categories using Blast2GO (version 2.3.5) (http://www.blast2go.org/). The annotations were verified manually and integrated using gene ontology (GO) classification (http://www.geneontology.org). Of 27,190 detected genes, 18,307 were categorized into 53 functional groups based on sequence homology. In each of the three main categories (biological process, molecular function, and cellular component) of the GO classification, there were 16, 17, and 20 functional groups, respectively (Figure 3). Metabolic process (GO: 0008152), with 851 genes, were dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, were dominant in the main categories of molecular function and cellular component, respectively. We also noticed a high percentage of genes from functional groups of cellular process (GO: 0009987) with 803 genes, nucleic acid binding (GO: 0003676) with 2725 genes, and intracellular (GO: 0005622) consisted of 1809 genes in the three main categories, respectively (Figure 3).


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

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

Histogram presentation of gene ontology (GO) classification.The results are summarized in three main categories: biological process, molecular function and cellular component. The y-axis indicates the number of genes in a category. In three main categories of GO classification, there are 16, 17, and 20 functional groups, respectively. Metabolic process (GO: 0008152), with 851 genes, are dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, are dominant in the main categories of molecular function and cellular component, respectively.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3275597&req=5

pone-0030646-g003: Histogram presentation of gene ontology (GO) classification.The results are summarized in three main categories: biological process, molecular function and cellular component. The y-axis indicates the number of genes in a category. In three main categories of GO classification, there are 16, 17, and 20 functional groups, respectively. Metabolic process (GO: 0008152), with 851 genes, are dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, are dominant in the main categories of molecular function and cellular component, respectively.
Mentions: To facilitate the global analysis of gene expression, all predicted rice genes were assigned to different functional categories using Blast2GO (version 2.3.5) (http://www.blast2go.org/). The annotations were verified manually and integrated using gene ontology (GO) classification (http://www.geneontology.org). Of 27,190 detected genes, 18,307 were categorized into 53 functional groups based on sequence homology. In each of the three main categories (biological process, molecular function, and cellular component) of the GO classification, there were 16, 17, and 20 functional groups, respectively (Figure 3). Metabolic process (GO: 0008152), with 851 genes, were dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, were dominant in the main categories of molecular function and cellular component, respectively. We also noticed a high percentage of genes from functional groups of cellular process (GO: 0009987) with 803 genes, nucleic acid binding (GO: 0003676) with 2725 genes, and intracellular (GO: 0005622) consisted of 1809 genes in the three main categories, respectively (Figure 3).

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