Full-length sequencing of Ginkgo biloba L. reveals the synthesis of terpenoids during seed development
Full-length sequencing of Ginkgo biloba L. reveals the synthesis of terpenoids during seed development
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DOI：
10.1016/j.indcrop.2021.113714
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发表时间：
2021-06-09
影响因子：
5.9
通讯作者：
Xu, Li-an
中科院分区：
文献类型：
--
作者：
Han, Xin;He, Bing;Xu, Li-an
基于PacBio测序平台的全长转录组测序可以显着优化基因结构的注释。银杏是银杏目单型裸子植物的古老孑遗植物，含有丰富的萜类化合物，具有药用价值。种子内含丰富的食用胚乳，味道鲜美，营养价值高。然而，现有对银杏种子发育过程的分子研究还比较薄弱，种子中萜类化合物的生物合成很少受到关注。因此，结合单分子实时（SMRT）技术和Illumina测序，对银杏生殖生长发育相关的6个组织进行测序，以生成高质量的全长转录数据库。总共获得了 20.98 Gb 的干净读数，其中包含 178,548 个全长非嵌合 (FLNC) 序列。从这些数据中，预测了4019个新基因和22,845个新亚型，注释了52.32%的新基因，并在萜烯合成相关途径中注释了3个新亚型。差异表达基因（DEG）富集分析显示，95个基因富集到与种子发育相关的21类，47个DEG富集于萜烯合成的骨骼途径。结合实时定量逆转录PCR（qRT-PCR），合成萜烯前体的磷酸合酶家族成员在种子发育过程中具有多样且复杂的表达趋势。我们的研究结果证实了SMRT的优势，有助于构建丰富的银杏种子发育研究转录数据集，丰富银杏基因组的注释，增强我们对银杏种子萜烯生物合成基因调控的理解。
Full-length transcriptome sequencing based on the PacBio sequencing platform could significantly optimize the annotation of gene structures. As an ancient relic gymnosperm in the monotypic order Ginkgoales, Ginkgo biloba L. contains rich terpenoids that are medicinally valuable. The seeds have abundant edible endosperm, which is delicious and of high nutritional value. However, existing molecular studies on the developmental process of ginkgo seeds are relatively weak, and the biosynthesis of terpenoids in seeds has received little attention. Therefore, single-molecule real-time (SMRT) technology and Illumina sequencing were combined to sequence six tissues related to the reproductive growth and development of ginkgo in order to generate a high-quality fulllength transcription database. In total, 20.98 Gb of clean reads containing 178,548 full-length non-chimeric (FLNC) sequences were obtained. From these data, 4019 novel genes and 22,845 novel isoforms were predicted, 52.32 % of the novel genes were annotated, and three novel isoforms were annotated in terpene synthesis related pathways. The enrichment analysis of differentially expressed genes (DEGs) showed that, 95 genes were enriched into 21 categories related to seed development, and 47 DEGs were enriched in the skeletal pathway of terpene synthesis. Combined with the real-time quantitative reverse transcription PCR (qRT-PCR), the phosphosynthase family members synthesizing terpene precursors have diverse and complex expression trends during seed development. Our findings confirm the advantages of SMRT, which facilitated the construction a rich transcript data-set for research on the development of ginkgo seeds, enriching the annotation of the ginkgo genome, and enhancing our understanding of gene regulation of terpene biosynthesis in ginkgo seeds.