Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis

Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.

蒙古黄芪（Astragalus membranaceus）在中国俗称黄芪，是传统中医药（Traditional Chinese Medicine）中应用最为广泛的药用草本植物之一。以蒙古黄芪为原料的中药方剂，已被用于治疗多种疾病，涵盖心血管疾病、2型糖尿病、肾炎及癌症等。药理学研究表明，蒙古黄芪提取物具备免疫调节、降血糖、抗炎、抗氧化及抗病毒等多种药理活性。因此，解析蒙古黄芪中活性成分的生物合成途径——例如黄芪皂苷（Astragalosides）、毛蕊异黄酮（Calycosin）以及毛蕊异黄酮-7-O-β-D-葡萄糖苷（Calycosin-7-O-β-D-glucoside）——对于开展蒙古黄芪的后续遗传学研究具有重要意义。本研究利用PacBio Iso-Seq长读长测序技术，对蒙古黄芪的叶和根组织进行了全长转录组重构。我们分别在这两种组织中鉴定出27975和22343个全长唯一转录本模型。相较于此前采用短读长测序技术的相关研究，本研究重构得到的转录本长度更长、更趋近于全长，且涵盖了大量转录本变异体。此外，我们还重新解析并鉴定了参与黄芪皂苷、毛蕊异黄酮及毛蕊异黄酮-7-O-β-D-葡萄糖苷生物合成的基因的潜在转录本变异体。综上，本研究为无参考基因组物种的全长转录组解析提供了一套实用的分析流程，同时也为探索蒙古黄芪活性成分的生物合成途径提供了宝贵的基因组学资源。