School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
Sci Rep. 2018 Jun 15;8(1):9211. doi: 10.1038/s41598-018-27493-z.
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.
植物茎系统由生殖器官组成，如花序、芽和果实，以及营养叶和茎。在这项研究中，研究了麻疯树茎系统的生殖部分，包括地上茎、花序和花序承载的茎，以探讨与产量相关的生物过程的基因间相互作用。在 Illumina HiSeq. 2500 平台上进行的基于 RNA-seq 的茎组织测序产生了 18 个转录组。使用基于参考基因组的映射方法，总共在所有样本中鉴定出 64361 个基因，并且通过 BLAST2GO Pro 套件将数据注释到非冗余数据库。去除异常值基因和样本后，共 17 个样本中的 12734 个基因用于使用 petal（一个 R 库）构建基因共表达网络。使用 scale-free 和 small-world 特性构建的基因共表达网络模型提取了四个附近网络（VN），它们可能与与产量相关的生物过程有关，分别为：热应激耐受、花和茎分生组织分化、叶绿素分子和乳管生物合成、细胞壁代谢和表观遗传调控。我们的 VN 揭示了一些可能的关键参与者，这些参与者可以适应麻疯树茎系统改良的育种策略。
