Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development

doi:10.1186/s12918-018-0574-x

	Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development
	Shen, Fangzhou ; Wu, Xueting 1; Shi, Luoxi 2,3; Zhang, Hang 2; Chen, Yangmin 2; Qi, Xiaoquan4 ; Wang, Zhuo 2; Li, Xuan 1
	2018
发表期刊	BMC SYSTEMS BIOLOGY
ISSN	1752-0509
卷号	12
摘要	Background: Rice (Oryza sativa) is one of the most important grain crops, which serves as food source for nearly half of the world population. The study of rice development process as well as related strategies for production has made significant progress. However, the comprehensive study on development of different rice tissues at both transcriptomic and metabolic flux level across different stages was lacked. Results: In this study, we performed RNA-Seq and characterized the expression profiles of differentiated tissues from Oryza sativa Zhonghua 11, including leaves, sheath, stamen, pistil, lemma and palea of the booting stage, and embryo, endosperm, lemma and palea of the mature grain stage. By integrating this set of transcriptome data of different rice tissues at different stages with a genome-scale rice metabolic model, we generated tissue-specific models and investigated the shift of metabolic patterns, and the discrepancy between transcriptomic and metabolic level. We found although the flux patterns are not very similar with the gene expression pattern, the tissues at booting stage and mature grain stage can be separately clustered by primary metabolism at either level. While the gene expression and flux distribution of secondary metabolism is more diverse across tissues and stages. The critical rate-limiting reactions and pathways were also identified. In addition, we compared the patterns of the same tissue at different stages and the different tissues at same stage. There are more altered pathways at gene expression level than metabolic level, which indicate the metabolism is more robust to reflect the phenotype, and might largely because of the complex post-transcriptional modification. Conclusions: The tissue-specific models revealed more detail metabolic pattern shift among different tissues and stages, which is of great significance to uncover mechanism of rice grain development and further improve production and quality of rice.
关键词	Transcriptome Metabolic flux Tissue-specific model Rice development Secondary metabolism
学科领域	Mathematical & Computational Biology
DOI	10.1186/s12918-018-0574-x
收录类别	SCI
语种	英语
WOS关键词	CELL-DIFFERENTIATION ; ARABIDOPSIS-THALIANA ; BALANCE ANALYSIS ; PLANT-GROWTH ; RIBOFLAVIN ; NETWORK ; GERMINATION ; PATHOGEN
WOS记录号	WOS:000430984100014
出版者	BIOMED CENTRAL LTD
文献子类	Article; Proceedings Paper
出版地	LONDON
资助机构	National Key Research and Development Plan of China [2016YFC0902403, 2017YFSF090159] ; Ministry of Agriculture of ChinaMinistry of Agriculture, China [2016ZX08010-002] ; Special Fund for strategic pilot technology Chinese Academy of Sciences [XDA08020104] ; Shanghai Natural Science Funding [16ZR1449700] ; Scientific Research Foundation for the Returned Overseas Chinese Scholars of the State Education MinistryScientific Research Foundation for the Returned Overseas Chinese Scholars [15Z102050028] ; open project from Synthetic Biology Key Laboratory of Chinese Academy of Sciences
作者邮箱	zhuowang@sjtu.edu.cn ; lixuan@sibs.ac.cn
作品OA属性	Green Published, gold
引用统计	被引频次：13[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/20397
专题	中科院植物分子生理学重点实验室
作者单位	1.Shanghai Jiao Tong Univ, Bio X Inst, Key Lab Genet Dev & Neuropsychiat Disorders, Minist Educ, Shanghai 200030, Peoples R China 2.Chinese Acad Sci, CAS Ctr Excellence Mol Plant Sci, Inst Plant Physiol & Ecol, Key Lab Synthet Biol,Shanghai Inst Biol Sci, Shanghai 200032, Peoples R China 3.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai 200240, Peoples R China 4.Univ Minnesota, Sch Publ Hlth, Div Biostat, Minneapolis, MN 55455 USA 5.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Shen, Fangzhou,Wu, Xueting,Shi, Luoxi,et al. Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development[J]. BMC SYSTEMS BIOLOGY,2018,12.
APA	Shen, Fangzhou.,Wu, Xueting.,Shi, Luoxi.,Zhang, Hang.,Chen, Yangmin.,...&Li, Xuan.(2018).Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development.BMC SYSTEMS BIOLOGY,12.
MLA	Shen, Fangzhou,et al."Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development".BMC SYSTEMS BIOLOGY 12(2018).

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
Shen-2018-Transcript（2744KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览请求全文