Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
G3 (Bethesda). 2021 Aug 7;11(8). doi: 10.1093/g3journal/jkab182.
Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.
山核桃富含生物活性成分，如脂肪酸（FAs）和类黄酮，是世界范围内重要的坚果类型。因此，山核桃中植物化学物质生物合成的分子机制是研究的重点。最近，已经公布了山核桃的基因组草图和几个转录组。然而，全长 mRNA 转录本仍不清楚，质量成分生物合成和积累的调控机制也尚未完全研究。在本研究中，使用单分子长读测序技术获得了山核桃仁的全长转录本。总共将 16702 个基因的 37504 个异构体映射到参考基因组上。已知异构体、新异构体和新异构体的数量分别为 9013 个（24.03%）、26080 个（69.54%）和 2411 个（6.51%）。超过 80%的转录本（30751 个，81.99%）具有功能注释。共检测到 15465 个选择性剪接（AS）事件和 65761 个选择性多聚腺苷酸化事件；其中，内含子保留是 AS 的主要类型（5652 个，36.55%）。此外，使用生物信息学方法预测了 1894 个长非编码 RNA 和 1643 个转录因子。最后，对与 FA 和类黄酮生物合成相关的结构基因进行了表征。在 FA 合成相关基因中观察到 AS 准确性的高频率（70.31%）。本研究提供了山核桃仁的全长转录组数据集，这将显著增强对山核桃仁成熟过程中植物化学物质生物合成调控基础的理解。
