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 (TCM). Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of A. membranaceus. Therefore, characterisating the biosynthesis of bioactive compounds in A. membranaceus, such as Astragalosides (AST), Calycosin and Calycosin-7-O-ß-D-glucoside (CG), is of particular importance for further genetic studies of A. membranaceus. In this study, we reconstructed the A. membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. High-quality RNAs (RNA integrity number > 7.0) were used for cDNA synthesis and library preparation. Two size bins were fractionated for each tissue: 1-2 and 2-3 kb. Three and five SMRT cells were used for sequencing 1-2 kb and 2-3 kb libraries for each tissue respectively using PacBio RS II platform with P6-P4 chemistry.