Dissecting organ-specific transcriptomes through RNA-sequencing
文献类型：期刊论文
| 作者 | Guan, Shan; Lu, Yingqing
|
| 刊名 | PLANT METHODS
 |
| 出版日期 | 2013 |
| 卷号 | 9 |
| 关键词 | Paired-end reads Transcriptome assembly Organ development Molecular network Within-genet genomic variation |
| ISSN号 | 1746-4811 |
| DOI | 10.1186/1746-4811-9-42 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| 学科主题 | Biochemical Research Methods ; Plant Sciences |
| 出版地 | LONDON |
| 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) |
| 语种 | 英语 |
| WOS记录号 | WOS:000329234400001 |
| 出版者 | BMC |
| 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) |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/27851]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 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). |
入库方式： OAI收割
来源：植物研究所
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