Abstract
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.
Highlights
Astragalus membranaceus, a member of the legume family, is one of the most commonly used herbs in Traditional Chinese Medicine (TCM) [1].A. membranaceus, known as ‘Huangqi’, is mainly grown in the northern regions of China as well as in Mongolia and Korea [2]
To compare the transcripts produced by different sequencing platforms, we looked at complete open reading frames (ORFs) from Isoform sequencing (Iso-Seq) consensus transcripts and Illumina de novo assembled transcripts aligned against a wellcurated full-length protein database, UniProt Knowledgebase (UniProtKB)
Compared with Illumina de novo assembled transcripts, a significantly higher percentage of Iso-Seq consensus isoforms contained full-length ORFs or near full-length ORFs (Figure 1b). These results demonstrate that PacBio Iso-Seq is an efficient strategy to generate HQ full-length transcripts without assembly, an element of critical importance for genomic studies on species without a reference genome assembly
Summary
Astragalus membranaceus, a member of the legume family, is one of the most commonly used herbs in Traditional Chinese Medicine (TCM) [1]. A. membranaceus, known as ‘Huangqi’ ( refers to the dried root of A. membranaceus), is mainly grown in the northern regions of China as well as in Mongolia and Korea [2]. The major bioactive components of A. membranaceus root extract are triterpenoid saponins, flavonoids and polysaccharides [2, 4,5,6,7]. To provide resources for future molecular barcoding and plant breeding, we have to understand the biosynthetic pathways of these bioactive compounds and characterise the corresponding key genes important for A. membranaceus-related TCM formulations
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