Dissecting organ-specific transcriptomes through RNA-sequencing

doi:10.1186/1746-4811-9-42

	Dissecting organ-specific transcriptomes through RNA-sequencing
	Guan, Shan; Lu, Yingqing
	2013
发表期刊	PLANT METHODS
ISSN	1746-4811
卷号	9
摘要	Background: Organ-specific gene expression contains rich information about in vivo biological processes. This kind of information, previously gathered through microarray profiling, has been proven fruitful to the understanding of specific mutants, regulatory events, signaling, and development. With the advent of the next-generation sequencing (NGS) of RNAs, more quantitative and detailed information of gene expressions than previously available can now be collected for each organ or organ developmental stages. The combination of an object-oriented experimental design and an efficient treatment of the high volume information generated through a NGS platform may offer a powerful tool for inferring previously intractable developmental processes. Results: We collected transcriptomic data over a Solexa/Illumina platform on samples of Ipomoea leaf, sepal, and petals (at three developmental stages), and presented a method for analyzing transcriptomic variations within and between organs. We demonstrated that in vivo signals of transcriptomes can be retrieved de novo through the NGS techniques, proper data handling, bioinformatic tools, and the current understanding of molecular networks. We found that numbers of transcribed genes from both nuclear and chloroplast genomes decreased by the same order of leaf -> sepal -> petal. Petal resembled leaf in cell division patterns and abundance level of commonly expressed organelle genes. Its chloroplast transcripts constituted a subset of those in leaf. Moreover, reconstructions of multiple metabolic networks for each organ enabled inferences of substance flow, providing transcript evidence for the path of sucrose in leaf to anthocyanin synthesis in petal. Conclusion: Our results attest that developmental transcriptomes are highly informative for exploring connections between morphological traits and the associated molecular networks. Significant hypotheses have been developed, including that the petal is a derived organ of leaf and that its color can be modified by fluctuations of substance flow within the associated metabolic networks among organs.
关键词	Paired-end reads Transcriptome assembly Organ development Molecular network Within-genet genomic variation
学科领域	Biochemical Research Methods ; Plant Sciences
DOI	10.1186/1746-4811-9-42
收录类别	SCI
语种	英语
WOS关键词	GENE-EXPRESSION ; FLOWER DEVELOPMENT ; IPOMOEA-PURPUREA ; SEQ DATA ; ANTHOCYANIN BIOSYNTHESIS ; MORNING GLORY ; ARABIDOPSIS ; EVOLUTION ; GENOME ; PETAL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000329234400001
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	Chinese Academy of Sciences(Chinese Academy of Sciences) ; National Science Foundation of China(National Natural Science Foundation of China (NSFC)) ; Ministry of Science and Technology(Ministry of Science, ICT & Future Planning, Republic of Korea)
作品OA属性	Green Accepted, gold, Green Published
引用统计	被引频次：10[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/2S10CLM1/27851
专题	系统与进化植物学国家重点实验室
作者单位	Chinese Acad Sci, State Key Lab Systemat & Evolutionary Bot, Inst Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Guan, Shan,Lu, Yingqing. Dissecting organ-specific transcriptomes through RNA-sequencing[J]. PLANT METHODS,2013,9.
APA	Guan, Shan,&Lu, Yingqing.(2013).Dissecting organ-specific transcriptomes through RNA-sequencing.PLANT METHODS,9.
MLA	Guan, Shan,et al."Dissecting organ-specific transcriptomes through RNA-sequencing".PLANT METHODS 9(2013).

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