Chromosome Level Genome Assembly of Andrographis paniculata

Ying Liang; Shanshan Chen; Kunhua Wei; Zijiang Yang; Shengchang Duan; Yuan Du; Peng Qu; Jianhua Miao; Wei Chen; Yang Dong

doi:10.3389/fgene.2020.00701

Chromosome Level Genome Assembly of Andrographis paniculata

Front Genet. 2020 Jun 30:11:701. doi: 10.3389/fgene.2020.00701. eCollection 2020.

Authors

Ying Liang¹, Shanshan Chen², Kunhua Wei¹, Zijiang Yang³, Shengchang Duan⁴, Yuan Du⁴, Peng Qu¹, Jianhua Miao¹, Wei Chen^{5

6

7}, Yang Dong^{1

3

5

7}

Affiliations

¹ Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
² BGI College, Zhengzhou University, Zhengzhou, China.
³ National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.
⁴ NowBio Biotechnology Company, Kunming, China.
⁵ State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
⁶ College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.
⁷ Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China.

Abstract

Andrographis paniculata (Chinese name: Chuanxinlian) is an annual dicotyledonous medicinal plant widely grown in China and Southeast Asia. The dried plant has a highly acclaimed usage in the traditional Chinese medicine for its antipyretic, anti-inflammatory, and analgesic effects. In order to help delineate the biosynthetic pathways of various secondary metabolites, we report in this study a high-quality reference genome for A. paniculata. With the help of both PacBio single molecule real time sequencing and Illumina sequencing reads for error correction, the A. paniculata genome was assembled into a total size of 284 Mb with a contig N50 size of 5.14 Mb. The contigs were further assembled into 24 pseudo-chromosomes by the Hi-C technique. We also analyzed the gene families (e.g., KSL, and CYP450) whose protein products are essential for synthesizing bioactive compounds in A. paniculata. In conclusion, the high-quality A. paniculata genome assembly builds the foundation for decoding the biosynthetic pathways of various medicinal compounds.

Keywords: Andrographis paniculata; Hi-C; PacBio sequencing; genome assembly; medicinal plant.