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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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Autores principales: E, Zhi-guo, Wang, Lei, Qin, Ryan, Shen, Haihong, Zhou, Jianhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929188/
https://www.ncbi.nlm.nih.gov/pubmed/24672392
http://dx.doi.org/10.1155/2014/917292
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author E, Zhi-guo
Wang, Lei
Qin, Ryan
Shen, Haihong
Zhou, Jianhua
author_facet E, Zhi-guo
Wang, Lei
Qin, Ryan
Shen, Haihong
Zhou, Jianhua
author_sort E, Zhi-guo
collection PubMed
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.
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spelling pubmed-39291882014-03-26 Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C E, Zhi-guo Wang, Lei Qin, Ryan Shen, Haihong Zhou, Jianhua ScientificWorldJournal Research Article 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. Hindawi Publishing Corporation 2014-01-29 /pmc/articles/PMC3929188/ /pubmed/24672392 http://dx.doi.org/10.1155/2014/917292 Text en Copyright © 2014 Zhi-guo E et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
E, Zhi-guo
Wang, Lei
Qin, Ryan
Shen, Haihong
Zhou, Jianhua
Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C
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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929188/
https://www.ncbi.nlm.nih.gov/pubmed/24672392
http://dx.doi.org/10.1155/2014/917292
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