title: Genome-wide characterisation of gene expression in rice leaf blades at 25 °C and 30 °C.
abstract: 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.
authors.affiliation: China National Rice Research Institute, No. 359, Tiyuchang Road, Hangzhou 310006, China.
authors.forename: Zhi-guo
authors.initials: ZG
authors.lastname: E
authors.affiliation: China National Rice Research Institute, No. 359, Tiyuchang Road, Hangzhou 310006, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: iBioinfo Group, Lexington, MA 02421, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Qin
authors.affiliation: School of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
authors.forename: Haihong
authors.initials: H
authors.lastname: Shen
authors.affiliation: Nantong University, Nantong 226001, China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Zhou
mesh_terms: D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D055106:Genome-Wide Association Study; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics*; D013696:Temperature; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D014157:Transcription Factors