Ginkgo biloba L. is regarded as the most ancient living tree, and its kernel has been used as a traditional Chinese medicine for more than 2,000 years. The leaf extracts of this tree have been among the bestselling herbal remedies in Western countries since the last century. To understand the biosynthesis of the pharmacologically active ingredients in G. biloba, flavonoids and terpenoid trilactones (TTLs), we sequenced the transcriptomes of G. biloba leaves, kernels and testae with Iso-Seq and RNA-Seq technologies and obtained 152,524 clean consensus reads. When these reads were used to improve the annotation of the G. biloba genome, 4,856 novel genes, 25,583 new isoforms of previously annotated genes and 4,363 lncRNAs were discovered. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that genes involved in growth, regulation and response to stress were more likely to be regulated by alternative splicing (AS) or alternative polyadenylation (APA), which represent the two most important posttranscriptional regulation mechanisms. It was found that some of the characterized genes involved in the biosynthesis of flavonoids and TTLs were also possibly regulated by AS and APA. Using phylogenetic and gene expression pattern analyses, some candidate genes for the biosynthesis of flavonoids and TTLs were screened. After qRT-PCR validation, the final candidate genes for flavonoid biosynthesis included three UDP-glycosyltransferases and one MYB transcription factor, while the candidate genes for TTL biosynthesis included two cytochrome P450 and one WRKY transcription factor. Our study suggested that Iso-Seq may play an important role in improving genome annotation, elucidating AS and APA mechanisms and discovering candidate genes involved in the biosynthesis of some secondary metabolites.

银杏树被认为是最古老的活树，其内核已被用作传统中药已有2000多年的历史了。自上个世纪以来，该树的叶提取物一直是西方国家最畅销的草药之一。为了了解银杏叶，黄酮类和萜类三内酯（TTLs）中药理活性成分的生物合成，我们用Iso-Seq和RNA-Seq技术对银杏叶，叶和睾丸的转录组进行了测序，并获得152,524个清晰的共有读。当这些读物用于改善银杏的注释时基因组，4,856个新基因，25,583个先前注释的基因的新亚型和4,363个lncRNA。基因本体论和《京都议定书》的《基因与基因组百科全书》分析表明，参与生长，调控和对应激反应的基因更有可能受到替代剪接（AS）或替代聚腺苷酸化（APA）的调控，这代表着两个最重要的转录后调控机制。已经发现，参与类黄酮和TTL生物合成的某些特征基因也可能受AS和APA的调节。使用系统发育和基因表达模式分析，筛选了用于生物合成类黄酮和TTL的一些候选基因。经过qRT-PCR验证后，类黄酮生物合成的最终候选基因包括3个UDP-糖基转移酶和1个MYB转录因子，而TTL生物合成的候选基因包括2个细胞色素P450和1个WRKY转录因子。我们的研究表明，Iso-Seq可能在改善基因组注释，阐明AS和APA机制以及发现参与某些次生代谢物生物合成的候选基因中起重要作用。