Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume

Abstract

SUMMARYChinese liquorice/licorice (Glycyrrhiza uralensis) is a leguminous plant species whose roots and rhizomes have been widely used as a herbal medicine and natural sweetener. Whole-genome sequencing is essential for gene discovery studies and molecular breeding in liquorice. Here, we report a draft assembly of the approximately 379-Mb whole-genome sequence of strain 308-19 of G. uralensis; this assembly contains 34 445 predicted protein-coding genes. Comparative analyses suggested well-conserved genomic components and collinearity of gene loci (synteny) between the genome of liquorice and those of other legumes such as Medicago and chickpea. We observed that three genes involved in isoflavonoid biosynthesis, namely, 2-hydroxyisoflavanone synthase (CYP93C), 2,7,4 0 -trihydroxyisoflavanone 4 0 -O-methyltransferase/isoflavone 4 0 -O-methyltransferase (HI4OMT) and isoflavone-7-O-methyltransferase (7-IOMT) formed a cluster on the scaffold of the liquorice genome and showed conserved microsynteny with Medicago and chickpea. Based on the liquorice genome annotation, we predicted genes in the P450 and UDP-dependent glycosyltransferase (UGT) superfamilies, some of which are involved in triterpenoid saponin biosynthesis, and characterised their gene expression with the reference genome sequence. The genome sequencing and its annotations provide an essential resource for liquorice improvement through molecular breeding and the discovery of useful genes for engineering bioactive components through synthetic biology approaches.

Multi‐tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome

“…A similar clade can be observed, including soybean GmSGT2 involved in transferring a galactosyl group from UDPgalactose to soyasapogenol B monoglucuronide (Shibuya et al, 2010) and five common bean candidates (Phvul.002G016400, Phvul.002G016500, Phvul.007G020600, Phvul.007G020700 and Phvul.007G020800). One common bean candidate (the candidate Phvul.010G101600) was identified in the cluster including MtUGT73K1, a UDP-glucosyltransferase shown to have specificity towards hederagenin and soyasapogenols B and E in Medicago (Achnine et al, 2005) and its putative counterpart in G. uralensis Glyur002597s00038050 (Mochida et al, 2017). Orthologs of these genes are only found in legumes, numbering between one and four copies in the species investigated ( Figure S7, UGT73K).…”

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

“…Whole-genome sequencing has become a practical strategy to identify metabolic pathways for natural product biosynthesis (Liu et al, 2017;Mochida et al, 2017), and genome sequences of members of the order Lamiales such as Salvia miltiorrhiza (Zhang et al, 2015;Xu et al, 2016), Salvia splendens (Dong et al, 2018), and Sesamum indicum (Zhang et al, 2013) make feasible the comparative analysis to investigate how RSFs are produced in Scutellaria.…”

Integrated omics analysis of specialized metabolism in medicinal plants

“…These findings, therefore, make the mining of genomic sequences for the identification of metabolic gene clusters a promising approach for the prediction and subsequent characterization of components of a biosynthetic pathway. Indeed, recent genomic sequences of important medicinal plants such as Catharanthus roseus (Kellner et al, 2015) and Glycyrrhiza uralensis (Mochida et al, 2017) have shown the existence of metabolic gene clusters, and further analysis may lead to new discoveries. Apart from metabolic gene clusters, genomics-facilitated genetic approaches for the discovery of metabolite pathways, including genome-wide association studies (GWAS) and expression quantitative trait loci (eQTLs), are important and have been successfully used in the model plant Arabidopsis and crops such as rice, maize and tomato among others (Brachi et al, 2011;Ingvarsson and Street, 2011;Pasam et al, 2012;Huang and Han, 2014).…”