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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°...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2014
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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. |
format | Online Article Text |
id | pubmed-3929188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
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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