High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids

Yongle Hu; Dongna Ma; Shuju Ning; Qi Ye; Xuanxuan Zhao; Qiansu Ding; Pingping Liang; Guoqian Cai; Xiaomao Ma; Xia Qin; Daozhi Wei

doi:10.3389/fpls.2021.742420

High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids

Front Plant Sci. 2021 Sep 30:12:742420. doi: 10.3389/fpls.2021.742420. eCollection 2021.

Authors

Yongle Hu^{1

2

3}, Dongna Ma⁴, Shuju Ning⁵, Qi Ye¹, Xuanxuan Zhao¹, Qiansu Ding⁴, Pingping Liang⁴, Guoqian Cai¹, Xiaomao Ma¹, Xia Qin¹, Daozhi Wei¹

Affiliations

¹ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
² College of Ecology and Resource Engineering, Wuyi University, Wuyishan, China.
³ Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, Wuyishan, China.
⁴ Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.
⁵ College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.

Abstract

Strobilanthes cusia (Nees) Kuntze is an important plant used to process the traditional Chinese herbal medicines "Qingdai" and "Nanbanlangen". The key active ingredients are indole alkaloids (IAs) that exert antibacterial, antiviral, and antitumor pharmacological activities and serve as natural dyes. We assembled the S. cusia genome at the chromosome level through combined PacBio circular consensus sequencing (CCS) and Hi-C sequencing data. Hi-C data revealed a draft genome size of 913.74 Mb, with 904.18 Mb contigs anchored into 16 pseudo-chromosomes. Contig N50 and scaffold N50 were 35.59 and 68.44 Mb, respectively. Of the 32,974 predicted protein-coding genes, 96.52% were functionally annotated in public databases. We predicted 675.66 Mb repetitive sequences, 47.08% of sequences were long terminal repeat (LTR) retrotransposons. Moreover, 983 Strobilanthes-specific genes (SSGs) were identified for the first time, accounting for ~2.98% of all protein-coding genes. Further, 245 putative centromeric and 29 putative telomeric fragments were identified. The transcriptome analysis identified 2,975 differentially expressed genes (DEGs) enriched in phenylpropanoid, flavonoid, and triterpenoid biosynthesis. This systematic characterization of key enzyme-coding genes associated with the IA pathway and basic helix-loop-helix (bHLH) transcription factor family formed a network from the shikimate pathway to the indole alkaloid synthesis pathway in S. cusia. The high-quality S. cusia genome presented herein is an essential resource for the traditional Chinese medicine genomics studies and understanding the genetic underpinning of IA biosynthesis.

Keywords: Strobilanthes cusia; basic helix-loop-helix; indole alkaloid biosynthesis; lineage-specific genes; medicinal plant; whole-genome sequencing.