Genomics Division, National Institute of Agricultural Science, RDA, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si 54874, Jeollabuk-do, Korea.
Data Science Center, Insilicogen Inc., Yongin-si 16954, Gyeonggi-do, Korea.
Int J Mol Sci. 2018 Oct 16;19(10):3192. doi: 10.3390/ijms19103192.
The spp. ( (Corn poppy) and (Iceland poppy)) genera are ornamental and medicinal plants that are used for the isolation of alkaloid drugs. In this study, we generated 700 Mb of transcriptome sequences with the PacBio platform. They were assembled into 120,926 contigs, and 1185 (82.2%) of the benchmarking universal single-copy orthologs (BUSCO) core genes were completely present in our assembled transcriptome. Furthermore, using 128 Gb of Illumina sequences, the transcript expression was assessed at three stages of plant development (30, 60, and 90 days), from which we identified 137 differentially expressed transcripts. Furthermore, three co-occurrence heat maps are generated from 51 different plant genomes along with the transcriptome, i.e., secondary metabolite biosynthesis, isoquinoline alkaloid biosynthesis (BIA) pathway, and cytochrome. Sixty-nine transcripts in the BIA pathway along with 22 different alkaloids (quantified with LC-QTOF-MS/MS) were mapped into the BIA KEGG map (map00950). Finally, we identified 39 full-length cytochrome transcripts and compared them with other genomes. Collectively, this transcriptome data, along with the expression and quantitative metabolite profiles, provides an initial recording of secondary metabolites and their expression related to plant development. Moreover, these profiles could help to further detail the functional characterization of the various secondary metabolite biosynthesis and plant development associated problems.
该 spp.（罂粟和冰岛罂粟）属植物是观赏和药用植物，用于分离生物碱药物。在这项研究中，我们使用 PacBio 平台生成了 700 Mb 的转录组序列。它们被组装成 120926 个 contigs，并且 1185 个（82.2%）基准通用单拷贝同源物（BUSCO）核心基因完全存在于我们组装的转录组中。此外，使用 128 Gb 的 Illumina 序列，在 植物发育的三个阶段（30、60 和 90 天）评估了转录表达，从中我们鉴定出 137 个差异表达的转录本。此外，从 51 种不同的植物基因组以及 转录组生成了三个共现热图，即次生代谢物生物合成、异喹啉生物碱生物合成（BIA）途径和细胞色素。BIA 途径中的 69 个转录本以及 22 种不同的生物碱（用 LC-QTOF-MS/MS 定量）被映射到 BIA KEGG 图谱（map00950）。最后，我们鉴定了 39 个全长细胞色素转录本，并与其他基因组进行了比较。总之，这些转录组数据以及表达和定量代谢物谱，提供了次生代谢物及其与 植物发育相关表达的初步记录。此外，这些图谱可以帮助进一步详细描述各种次生代谢物生物合成和 植物发育相关问题的功能特征。
