Li Jun, Harata-Lee Yuka, Denton Matthew D, Feng Qianjin, Rathjen Judith R, Qu Zhipeng, Adelson David L
Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
Zhendong Center for the Molecular Basis of Traditional Chinese Medicine, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
Cell Discov. 2017 Aug 29;3:17031. doi: 10.1038/celldisc.2017.31. eCollection 2017.
also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from 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 . Therefore, characterising the biosynthesis of bioactive compounds in , such as Astragalosides, Calycosin and Calycosin-7-O-β-d-glucoside, is of particular importance for further genetic studies of . In this study, we reconstructed the 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 .
在中国也被称为黄芪，是传统中药中使用最广泛的草药之一。来自传统中药配方已被用于治疗多种疾病，如心血管疾病、2型糖尿病、肾炎和癌症。药理研究表明，黄芪提取物具有免疫调节、抗高血糖、抗炎、抗氧化和抗病毒活性。因此，表征黄芪中生物活性化合物的生物合成，如黄芪皂苷、毛蕊异黄酮和毛蕊异黄酮-7-O-β-D-葡萄糖苷，对于黄芪的进一步遗传研究尤为重要。在本研究中，我们使用PacBio Iso-Seq长读长从叶片和根组织重建了黄芪全长转录组。我们在每个组织中分别鉴定出27975个和22343个全长独特转录本模型。与之前使用短读长测序的研究相比，我们重建的转录本更长，更可能是全长的，并且包含大量转录本变体。此外，我们还重新表征并鉴定了参与黄芪皂苷、毛蕊异黄酮和毛蕊异黄酮-7-O-β-D-葡萄糖苷生物合成的基因的潜在转录本变体。总之，我们的研究提供了一个实用的流程来表征无参考基因组物种的全长转录组，并为探索黄芪中活性化合物的生物合成提供了有用的基因组资源。
