Comparative analysis of the transcriptomes of two rice subspecies during domestication

Abstract Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of th...

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Autores principales: Hongbo Pang, Qiang Chen, Yueying Li, Ze Wang, Longkun Wu, Qingwen Yang, Xiaoming Zheng
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Publicado: Nature Portfolio 2021
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Acceso en línea:https://doaj.org/article/10fdaf6225f6441680d40f459af0ef4c
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spelling oai:doaj.org-article:10fdaf6225f6441680d40f459af0ef4c2021-12-02T13:30:17ZComparative analysis of the transcriptomes of two rice subspecies during domestication10.1038/s41598-021-83162-82045-2322https://doaj.org/article/10fdaf6225f6441680d40f459af0ef4c2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83162-8https://doaj.org/toc/2045-2322Abstract Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.Hongbo PangQiang ChenYueying LiZe WangLongkun WuQingwen YangXiaoming ZhengNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Hongbo Pang
Qiang Chen
Yueying Li
Ze Wang
Longkun Wu
Qingwen Yang
Xiaoming Zheng
Comparative analysis of the transcriptomes of two rice subspecies during domestication
description Abstract Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.
format article
author Hongbo Pang
Qiang Chen
Yueying Li
Ze Wang
Longkun Wu
Qingwen Yang
Xiaoming Zheng
author_facet Hongbo Pang
Qiang Chen
Yueying Li
Ze Wang
Longkun Wu
Qingwen Yang
Xiaoming Zheng
author_sort Hongbo Pang
title Comparative analysis of the transcriptomes of two rice subspecies during domestication
title_short Comparative analysis of the transcriptomes of two rice subspecies during domestication
title_full Comparative analysis of the transcriptomes of two rice subspecies during domestication
title_fullStr Comparative analysis of the transcriptomes of two rice subspecies during domestication
title_full_unstemmed Comparative analysis of the transcriptomes of two rice subspecies during domestication
title_sort comparative analysis of the transcriptomes of two rice subspecies during domestication
publisher Nature Portfolio
publishDate 2021
url https://doaj.org/article/10fdaf6225f6441680d40f459af0ef4c
work_keys_str_mv AT hongbopang comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
AT qiangchen comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
AT yueyingli comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
AT zewang comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
AT longkunwu comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
AT qingwenyang comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
AT xiaomingzheng comparativeanalysisofthetranscriptomesoftworicesubspeciesduringdomestication
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