Miao Liyun, Zhang Libin, Raboanatahiry Nadia, Lu Guangyuan, Zhang Xuekun, Xiang Jun, Gan Jianping, Fu Chunhua, Li Maoteng
School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China; Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China.
School of Life Science and Technology, Huazhong University of Science and Technology Wuhan, China.
Front Plant Sci. 2016 Sep 21;7:1403. doi: 10.3389/fpls.2016.01403. eCollection 2016.
is one of the most important oilseed crops in the world. However, there is currently no enough stem transcriptome information and comparative transcriptome analysis of different tissues, which impedes further functional genomics research on . In this study, the stem transcriptome of was characterized by RNA-seq technology. Approximately 13.4 Gb high-quality clean reads with an average length of 100 bp were generated and used for comparative transcriptome analysis with the existing transcriptome sequencing data of roots, leaves, flower buds, and immature embryos of . All the transcripts were annotated against GO and KEGG databases. The common genes in five tissues, differentially expressed genes (DEGs) of the common genes between stems and other tissues, and tissue-specific genes were detected, and the main biochemical activities and pathways implying the common genes, DEGs and tissue-specific genes were investigated. Accordingly, the common transcription factors (TFs) in the five tissues and tissue-specific TFs were identified, and a TFs-based regulation network between TFs and the target genes involved in 'Phenylpropanoid biosynthesis' pathway were constructed to show several important TFs and key nodes in the regulation process. Collectively, this study not only provided an available stem transcriptome resource in , but also revealed valuable comparative transcriptome information of five tissues of for future investigation on specific processes, functions and pathways.
是世界上最重要的油料作物之一。然而，目前尚无足够的茎转录组信息以及不同组织的比较转录组分析，这阻碍了对其进一步的功能基因组学研究。在本研究中，利用RNA测序技术对的茎转录组进行了表征。产生了约13.4 Gb高质量的干净 reads，平均长度为100 bp，并用于与现有的根、叶、花芽和未成熟胚的转录组测序数据进行比较转录组分析。所有转录本均根据GO和KEGG数据库进行注释。检测了五个组织中的共同基因、茎与其他组织之间共同基因的差异表达基因（DEGs）以及组织特异性基因，并研究了暗示共同基因、DEGs和组织特异性基因的主要生化活性和途径。据此，鉴定了五个组织中的共同转录因子（TFs）和组织特异性TFs，并构建了基于TFs的调控网络，该网络涉及“苯丙烷生物合成”途径中的TFs与靶基因之间的关系，以展示调控过程中的几个重要TFs和关键节点。总的来说，本研究不仅提供了可用的茎转录组资源，还揭示了五个组织有价值的比较转录组信息，以供未来对特定过程、功能和途径进行研究。
