Chromosome‐level genome assembly and functional characterization of terpene synthases provide insights into the volatile terpenoid biosynthesis of Wurfbainia villosa

Abstract

SUMMARY Wurfbainia villosa is a well‐known medicinal and edible plant that is widely cultivated in the Lingnan region of China. Its dried fruits (called Fructus Amomi) are broadly used in traditional Chinese medicine for curing gastrointestinal diseases and are rich in volatile terpenoids. Here, we report a high‐quality chromosome‐level genome assembly of W. villosa with a total size of approximately 2.80 Gb, 42 588 protein‐coding genes, and a very high percentage of repetitive sequences (87.23%). Genome analysis showed that W. villosa likely experienced a recent whole‐genome duplication event prior to the W. villosa–Zingiber officinale divergence (approximately 11 million years ago), and a recent burst of long terminal repeat insertions afterward. The W. villosa genome enabled the identification of 17 genes involved in the terpenoid skeleton biosynthesis pathway and 66 terpene synthase (TPS) genes. We found that tandem duplication events have an important contribution to the expansion of WvTPSs, which likely drove the production of volatile terpenoids. In addition, functional characterization of 18 WvTPSs, focusing on the TPS‐a and TPS‐b subfamilies, showed that most of these WvTPSs are multi‐product TPS and are predominantly expressed in seeds. The present study provides insights into the genome evolution and the molecular basis of the volatile terpenoids diversity in W. villosa. The genome sequence also represents valuable resources for the functional gene research and molecular breeding of W. villosa.

Multi-omics Comparison among Populations of Three Plant Sources of Amomi Fructus

“…The length of 24 pseudochromosomes was from 151,371,763 (chr_01) to 66,131,911 bp (chr_24) (Figure 1B and Table S1). The genome size of WVV was almost the same as the published WVV genome size (2.80 Gb) 17 and 1.4∼2.9 times larger than that of other Zingiberaceae species 41-44 . The average GC content of WVV genome was 40.73% (Table 1).…”

“…Subsequently, we constructed the maximum-likelihood (ML) tree with TPS genes from WVV genome and the functionally verified TPS genes in previous study 17 . Based on the ML tree, 11 TPS genes, clustered with the verified ones, were selected (Figure S2).…”

“…Wv02G0592, Wvscaf10527, Wv11G1308 and Wv11G1312 were all bi-or multifunctional enzyme genes based on verified homologous genes 17 . We only knew the abundance trends of α-pinene, β-myrcene, and camphene of WVV and WVX, not that of β-pinene, limonene and bornyl diphosphate 21 .…”

“…To investigate the pattern of gene expression affecting the abundance of volatile compounds between the two subspecies, we analyzed the expression of genes involved in multiple terpenes biosynthesis in various tissues and fruit developmental stages between WVV and WVX (see Materials and Methods; Figure 2). Subsequently, we constructed the maximum-likelihood (ML) tree with TPS genes from WVV genome and the functionally verified TPS genes in previous study 17 . Based on the ML tree, 11 TPS genes, clustered with the verified ones, were selected (Figure S2).…”

“…In Chinese Pharmacopoeia, AF is described as the dry and mature fruit of 10 . It is one of the four most important Southern China Medicines, and a dual-purpose commodity for medicine and food [16][17][18] . It is well-known for its efficacy of soothing the fetus, stopping diarrhea and appetizing 10 , and the effective components are volatile oil, mainly terpenes, including monoterpenes (bornyl acetate, borneol, camphor, myrcene, limonene, α-terpinene, etc.)…”