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

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.

The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau

“… 53 , 54 However, the proportion of long terminal repeat retrotransposons (LTR-RTs), 21.68% of the genome, was considerably smaller than that for several previously published plant genomes, such as 43.6% for caper spurge ( Euphorbia lathyris ), 55 47.08% for Strobilanthes cusia . 56 Moreover, a consistent tendency for less proportion of LTR-RTs is possible in alpine sedges, for example, 27.87% ( K. littledalei ), 4 25.47% ( Carex parvula ), and 23.84% ( Carex kokanica ). 51 The reason for this pattern needs further investigation.…”

Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview

“…To extend the application field, we suggested the inclusion of medicinal orphan crops that also represent a secondary metabolite gold mine that deserves to be investigated. Among those orphan crops, the transcriptional comprehension of certain secondary metabolite synthesis has been initiated ( Kang et al, 2020 ; Hu et al, 2021 ; Wang et al, 2021a , b ) paving the way for not only effective JA triggered health-oriented metabolic engineering but also engineered crop protection against adverse biotic and abiotic stresses. Under the ongoing environmental change status, JAs’ mediated metabolite elicitation machinery needs further investigation in diverse plant systems.…”

Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

“…However, this characteristic is not universal. In Strobilanthes cusia , there was no difference in GC content ( Hu et al, 2021 ). In Aegiceras corniculatum and wheat, OGs were significantly less than that of NOGs ( Ma et al, 2021 ).…”