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

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

doi:10.3389/fpls.2021.742420

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.

Highlights

IntroductionThe phytochemical analyses showed that S. cusia can produce high quantities of biologically active compounds, such as, indole alkaloids (IAs), quinolone alkaloids, phenylethanoid glycosides, lignan glycosides, triterpenoids, steroids, amino acids, and flavonoids (Gu et al, 2014; Xiao et al, 2018; Yu et al, 2021)
Strobilanthes cusia (Nees) Kuntze (2n = 32) is a perennial dicotyledonous herb of the order Acanthaceae and is broadly distributed from South to East Asia, the countries such as, India, Bangladesh, Thailand, Bhutan, and China (Hu et al, 2011)
We generated 483.97 Gb (532×) of PacBio long circular consensus sequencing (CCS) reads and ∼49.98 Gb (53×) of Illumina clean reads (Supplementary Table 1) and used hifiasm to assemble the genome with 913.74 Mb that includes 1,357 contigs (N50 size of 35.59 Mb) with the longest contig of 66.79 Mb (Table 1)

Summary

Introduction

The phytochemical analyses showed that S. cusia can produce high quantities of biologically active compounds, such as, indole alkaloids (IAs), quinolone alkaloids, phenylethanoid glycosides, lignan glycosides, triterpenoids, steroids, amino acids, and flavonoids (Gu et al, 2014; Xiao et al, 2018; Yu et al, 2021). Among these chemical components, indigo and indirubin are the major medicinal ingredients and are isomers of each other (C16H10N2O2). Clinical and pharmacological evidence suggests that the main alkaloids can treat leukemia (Wang et al, 2008; Wu et al, 2016) and dermatoses (Hsieh et al, 2012); protect against tissue damage (Huang et al, 2017); and exert anti-inflammatory (Sugimoto et al, 2016; Kawai et al, 2017), antibacterial (Chiang et al, 2013; Tsai et al, 2020), and immune-regulatory effects (Zhang et al, 2015; Jie et al, 2017)

Methods

Results

Discussion

Conclusion