Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C
Rice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25°...
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1155/2014/917292 |
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| author | Zhi-guo E Lei Wang Ryan Qin Haihong Shen Jianhua Zhou |
| author_facet | Zhi-guo E Lei Wang Ryan Qin Haihong Shen Jianhua Zhou |
| author_sort | Zhi-guo E |
| collection | DOAJ |
| description | Rice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25°C and 30°C. Our analysis indicated that 50.4% of all genes in the rice genome (28,296/56,143) were expressed in rice samples grown at 25°C, whereas slightly fewer genes (50.2%; 28,189/56,143) were expressed in rice leaf blades grown at 30°C. Among the genes that were expressed, approximately 3% were highly expressed, whereas approximately 65% had low levels of expression. Further examination demonstrated that 821 genes had a twofold or higher increase in expression and that 553 genes had a twofold or greater decrease in expression at 25°C. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the ribosome pathway and multiple metabolic pathways were upregulated at 25°C. Based on these results, we deduced that gene expression at both transcriptional and translational levels was stimulated at 25°C, perhaps in response to a suboptimal temperature condition. Finally, we observed that temperature markedly regulates several super-families of transcription factors, including bZIP, MYB, and WRKY. |
| format | Article |
| id | doaj-art-dae973ba23ae4730a2d9a42f0d9c8fba |
| institution | OA Journals |
| issn | 2356-6140 1537-744X |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-dae973ba23ae4730a2d9a42f0d9c8fba2025-08-20T02:21:35ZengWileyThe Scientific World Journal2356-61401537-744X2014-01-01201410.1155/2014/917292917292Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°CZhi-guo E0Lei Wang1Ryan Qin2Haihong Shen3Jianhua Zhou4China National Rice Research Institute, No. 359, Tiyuchang Road, Hangzhou 310006, ChinaChina National Rice Research Institute, No. 359, Tiyuchang Road, Hangzhou 310006, ChinaiBioinfo Group, Lexington, MA 02421, USASchool of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of KoreaNantong University, Nantong 226001, ChinaRice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25°C and 30°C. Our analysis indicated that 50.4% of all genes in the rice genome (28,296/56,143) were expressed in rice samples grown at 25°C, whereas slightly fewer genes (50.2%; 28,189/56,143) were expressed in rice leaf blades grown at 30°C. Among the genes that were expressed, approximately 3% were highly expressed, whereas approximately 65% had low levels of expression. Further examination demonstrated that 821 genes had a twofold or higher increase in expression and that 553 genes had a twofold or greater decrease in expression at 25°C. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the ribosome pathway and multiple metabolic pathways were upregulated at 25°C. Based on these results, we deduced that gene expression at both transcriptional and translational levels was stimulated at 25°C, perhaps in response to a suboptimal temperature condition. Finally, we observed that temperature markedly regulates several super-families of transcription factors, including bZIP, MYB, and WRKY.http://dx.doi.org/10.1155/2014/917292 |
| spellingShingle | Zhi-guo E Lei Wang Ryan Qin Haihong Shen Jianhua Zhou Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C The Scientific World Journal |
| title | Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C |
| title_full | Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C |
| title_fullStr | Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C |
| title_full_unstemmed | Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C |
| title_short | Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C |
| title_sort | genome wide characterisation of gene expression in rice leaf blades at 25°c and 30°c |
| url | http://dx.doi.org/10.1155/2014/917292 |
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