Cargando…
Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf...
Autores principales: | , , , , , , , , , , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047585/ https://www.ncbi.nlm.nih.gov/pubmed/21407816 http://dx.doi.org/10.1371/journal.pone.0017613 |
_version_ | 1782199048883666944 |
---|---|
author | Xu, Wenying Yang, Rendong Li, Meina Xing, Zhuo Yang, Wenqiang Chen, Guang Guo, Han Gong, Xiaojie Du, Zhou Zhang, Zhenhai Hu, Xingming Wang, Dong Qian, Qian Wang, Tai Su, Zhen Xue, Yongbiao |
author_facet | Xu, Wenying Yang, Rendong Li, Meina Xing, Zhuo Yang, Wenqiang Chen, Guang Guo, Han Gong, Xiaojie Du, Zhou Zhang, Zhenhai Hu, Xingming Wang, Dong Qian, Qian Wang, Tai Su, Zhen Xue, Yongbiao |
author_sort | Xu, Wenying |
collection | PubMed |
description | Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. |
format | Text |
id | pubmed-3047585 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-30475852011-03-15 Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves Xu, Wenying Yang, Rendong Li, Meina Xing, Zhuo Yang, Wenqiang Chen, Guang Guo, Han Gong, Xiaojie Du, Zhou Zhang, Zhenhai Hu, Xingming Wang, Dong Qian, Qian Wang, Tai Su, Zhen Xue, Yongbiao PLoS One Research Article Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. Public Library of Science 2011-03-02 /pmc/articles/PMC3047585/ /pubmed/21407816 http://dx.doi.org/10.1371/journal.pone.0017613 Text en Xu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Xu, Wenying Yang, Rendong Li, Meina Xing, Zhuo Yang, Wenqiang Chen, Guang Guo, Han Gong, Xiaojie Du, Zhou Zhang, Zhenhai Hu, Xingming Wang, Dong Qian, Qian Wang, Tai Su, Zhen Xue, Yongbiao Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves |
title | Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves |
title_full | Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves |
title_fullStr | Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves |
title_full_unstemmed | Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves |
title_short | Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves |
title_sort | transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047585/ https://www.ncbi.nlm.nih.gov/pubmed/21407816 http://dx.doi.org/10.1371/journal.pone.0017613 |
work_keys_str_mv | AT xuwenying transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT yangrendong transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT limeina transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT xingzhuo transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT yangwenqiang transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT chenguang transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT guohan transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT gongxiaojie transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT duzhou transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT zhangzhenhai transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT huxingming transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT wangdong transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT qianqian transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT wangtai transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT suzhen transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves AT xueyongbiao transcriptomephasedistributionanalysisrevealsdiurnalregulatedbiologicalprocessesandkeypathwaysinriceflagleavesandseedlingleaves |