Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China.
Xinyang Agriculture and Forestry University, Xinyang, Henan 464000, China.
J Agric Food Chem. 2020 Dec 9;68(49):14670-14683. doi: 10.1021/acs.jafc.0c05381. Epub 2020 Nov 29.
Abel., belonging to the genus of Theaceae, has been widely used as a cooking oil, lubricant, and in cosmetics. Because of complicated polyploidization and large genomes, reference genome information is still lacking. Systematic characterization of gene models based on transcriptome data is a fast and economical approach for . Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq) and Illumina RNA-Seq combined with gas chromatography were performed for exploration of oil biosynthesis, accumulation, and comprehensive transcriptome analysis in seeds at five different developmental stages. We report the first full-length transcriptome data set of seeds comprising 40,143 deredundant high-quality isoforms. Among these isoforms, 37,982 were functionally annotated, and 271 (2.43%) belonged to fatty acid metabolism. A total of 8,344 full-length unique transcript models were obtained, and 8,151 (97.69%) of them produced more than two isoforms, suggesting a high degree of transcriptome complexity in seeds. A total of 783 alternative splicing (AS) events were identified, among which the retained intron was the most abundant. We also obtained 1,910 long noncoding RNAs (lncRNAs) and found that AS events occurred in these lncRNAs. Potential transcript variants of genes involved in oil biosynthesis were also investigated. After performing weighted correlation network analysis, we found seven "gene modules" and hub genes for each module showing a significant association with oil content. The series test of clusters classified these modules into four significant profiles based on gene expression patterns. Protein-protein interaction network analysis showed that upregulated interacted with 17 genes encoding the enzymes playing key roles in oil synthesis. and transcriptional factors also showed significant interactions with key genes involved in oil synthesis. Collectively, our data advance the knowledge of RNA isoform diversity in seeds at different developmental stages and provide a rich resource for functional studies on oil synthesis in .
榆绿木属植物隶属于山茶科，被广泛用作食用油、润滑剂和化妆品。由于其复杂的多倍化和庞大的基因组，参考基因组信息仍然缺乏。基于转录组数据对基因模型进行系统表征是一种快速而经济的方法，可用于植物基因组学研究。本研究采用太平洋生物科学公司的单分子长读长异构体测序（Iso-Seq）和 Illumina RNA-Seq 联合气相色谱法，对 5 个不同发育阶段的 种子中的油脂生物合成、积累和综合转录组进行了分析。我们报告了首个榆绿木种子全长转录组数据集，包含 40143 个冗余的高质量异构体。在这些异构体中，37982 个具有功能注释，其中 271 个（2.43%）属于脂肪酸代谢。共获得 8344 个全长独特转录本模型，其中 8151 个（97.69%）产生了超过两个异构体，表明 种子中转录组的复杂性很高。共鉴定出 783 个剪接事件，其中保留内含子最为丰富。我们还获得了 1910 个长非编码 RNA（lncRNA），并发现这些 lncRNA 中存在剪接事件。还研究了与油脂生物合成相关的基因的潜在转录变体。在进行加权相关网络分析后，我们发现了 7 个“基因模块”和每个模块的枢纽基因，它们与油脂含量呈显著相关。聚类的系列检验根据基因表达模式将这些模块分为四个显著的图谱。蛋白质-蛋白质相互作用网络分析表明，上调的 与 17 个编码在油脂合成中起关键作用的酶的基因相互作用。转录因子 与参与油脂合成的关键基因也表现出显著的相互作用。总之，我们的数据推进了不同发育阶段种子中 RNA 异构体多样性的知识，为榆绿木种子油脂合成的功能研究提供了丰富的资源。
