Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/115429
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Type: Journal article
Title: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
Author: Li, J.
Harata-Lee, Y.
Denton, M.
Feng, Q.
Rathjen, J.
Qu, Z.
Adelson, D.
Citation: Cell Discovery, 2017; 3:17031-1-17031-13
Publisher: Nature Publishing Group
Issue Date: 2017
ISSN: 2056-5968
2056-5968
Statement of
Responsibility: 
Jun Li, Yuka Harata-Lee, Matthew D Denton, Qianjin Feng, Judith R Rathjen, Zhipeng Qu, David L Adelson
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-beta-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-beta-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.
Keywords: Astragalus membranaceus; transcriptome; Iso-Seq; biosynthesis; alternative splicing
Rights: © The Author(s) 2017. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
RMID: 0030075111
DOI: 10.1038/celldisc.2017.31
Appears in Collections:Agriculture, Food and Wine publications

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