The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway.

Tianlin Pei,Yumin Fang,Mengying Cui,Binjie Ge,Qing Zhao,Hang Fan,Mengxiao Yan,Jie Liu,Yu Kong,Jun Yang

doi:10.46471/gigabyte.14

Abstract

Tripterygium wilfordii is a vine from the Celastraceae family that is used in traditional Chinese medicine (TCM). The active ingredient, celastrol, is a friedelane-type pentacyclic triterpenoid with putative roles as an antitumor, immunosuppressive, and anti-obesity agent. Here, we report a reference genome assembly of T. wilfordii with high-quality annotation using a hybrid sequencing strategy. The total genome size obtained is 340.12Mb, with a contig N50 value of 3.09Mb. We successfully anchored 91.02% of sequences into 23 pseudochromosomes using high-throughput chromosome conformation capture (Hi-C) technology. The super-scaffold N50 value was 13.03Mb. We also annotated 31,593 structural genes, with a repeat percentage of 44.31%. These data demonstrate that T. wilfordii diverged from Malpighiales species approximately 102.4million years ago. By integrating genome, transcriptome and metabolite analyses, as well as in vivo and in vitro enzyme assays of two cytochrome P450 (CYP450) genes, TwCYP712K1 and TwCYP712K2, it is possible to investigate the second biosynthesis step of celastrol and demonstrate that this was derived from a common ancestor. These data provide insights and resources for further investigation of pathways related to celastrol, and valuable information to aid the conservation of resources, as well as understand the evolution of Celastrales.

Highlights

Tripterygium wilfordii Hook. f. (NCBI: txid458696) is a perennial twining shrub belonging to the Celastraceae family
We provided a high-quality reference genome of T. wilfordii with a 340.12 Mb genome assembly (90.5% of the 375.84 Mb estimated genome size) and 3.09 Mb contig N50, and successfully anchored 91.02% of the sequences into 23 pseudochromosomes (Table 12)
The quality of our genome is close to that of the recently published T. wilfordii genome (348.38 Mb total contigs and 4.36 Mb contig N50), which was sequenced and assembled using Illumina, PacBio and highthroughput chromosome conformation capture (Hi–C) sequencing [86]. They identified a key CYP gene that can catalyze the oxidation of a methyl group to the acid moiety of dehydroabietic acid in triptolide biosynthesis, another clinically used specialized metabolite in T. wilfordii. Based on this genomic data, 35 CYP genes related to triterpenoid structure modification were identified according to phylogenetic analysis (Figure 8); 16 of these were co-expressed with TwOSC1 or TwOSC3 according to tissue-specific transcript profiles (Figures 11 and 12)

Summary

INTRODUCTION

Tripterygium wilfordii Hook. f. (NCBI: txid458696) is a perennial twining shrub belonging to the Celastraceae family. The potential medicinal activity of T. wilfordii has been studied since the 1960s, with its root being used to alleviate the symptoms of leprosy patients in Gutian County, Fujian Province, China [4]. This application ignited the interest of researchers in various fields. TwCYP712K1 and TwCYP712K2 were functionally characterized using in vivo yeast and in vitro enzyme assays These data represent a strategy to reveal the evolution of Celastrales and the key genes involved in celastrol biosynthesis

METHODS

RESULTS

DISCUSSION

AVAILABILITY OF DATA AND MATERIALS

64 Blum M et al The InterPro protein families and domains database