Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis

Abstract

Gynostemma pentaphyllum (Thunb.) Makino is an economically valuable medicinal plant belonging to the Cucurbitaceae family that produces the bioactive compound gypenoside. Despite several transcriptomes having been generated for G. pentaphyllum, a reference genome is still unavailable, which has limited the understanding of the gypenoside biosynthesis and regulatory mechanism. Here, we report a high-quality G. pentaphyllum genome with a total length of 582 Mb comprising 1,232 contigs and a scaffold N50 of 50.78 Mb. The G. pentaphyllum genome comprised 59.14% repetitive sequences and 25,285 protein-coding genes. Comparative genome analysis revealed that G. pentaphyllum was related to Siraitia grosvenorii, with an estimated divergence time dating to the Paleogene (∼48 million years ago). By combining transcriptome data from seven tissues, we reconstructed the gypenoside biosynthetic pathway and potential regulatory network using tissue-specific gene co-expression network analysis. Four UDP-glucuronosyltransferases (UGTs), belonging to the UGT85 subfamily and forming a gene cluster, were involved in catalyzing glycosylation in leaf-specific gypenoside biosynthesis. Furthermore, candidate biosynthetic genes and transcription factors involved in the gypenoside regulatory network were identified. The genetic information obtained in this study provides insights into gypenoside biosynthesis and lays the foundation for further exploration of the gypenoside regulatory mechanism.

Genome-Wide Identification of R2R3-MYB Transcription Factors: Discovery of a “Dual-Function” Regulator of Gypenoside and Flavonol Biosynthesis in Gynostemma pentaphyllum

“…Transcriptional activators usually present similar expression patterns to the downstream structural genes of the metabolic pathway, narrowing the scope of screening candidate regulators and providing functional prediction. In a previous study, the early biosynthesis genes (EBGs) and late biosynthesis genes (LBGs) corresponding to gypenoside biosynthesis were elucidated ( Huang et al, 2021 ). Furthermore, based on the gene expression profiles of different tissues (tendril, young leaf, mature leaf, root, stem, flower, and fruit), a WGCNA was performed to identify the potential upstream regulators of gypenoside biosynthetic pathway genes ( Huang et al, 2021 ).…”

“…In a previous study, the early biosynthesis genes (EBGs) and late biosynthesis genes (LBGs) corresponding to gypenoside biosynthesis were elucidated ( Huang et al, 2021 ). Furthermore, based on the gene expression profiles of different tissues (tendril, young leaf, mature leaf, root, stem, flower, and fruit), a WGCNA was performed to identify the potential upstream regulators of gypenoside biosynthetic pathway genes ( Huang et al, 2021 ). In the constructed gypenoside biosynthesis regulatory network, five GpMYB genes were identified, three of which were R2R3-MYB genes, including GpMYB60 , GpMYB80 , and GpMYB81 .…”

“…qRT-PCR was performed using the LightCycler 96 System (Roche, United States). The GpActin gene was used for quantitative gene expression normalization (Xu et al, 2020;Huang et al, 2021). The 2 − Ct analysis method was adopted to calculate 2 http://smart.embl-heidelberg.de/ the relative gene expression.…”

“…In contrast, flavonols extracted from G. pentaphyllum contain mainly kaempferol and quercetin derivatives, which were considered major contributors to the beneficial properties of G. pentaphyllum ( Xie et al, 2011 ). In a recent study, gypenoside biosynthetic genes, including farnesyl pyrophosphate synthase ( FPS ), squalene synthase ( SS ), squalene epoxidase ( SE ), 2,3-oxidosqualene cyclase ( OSC ), and cytochrome P450 ( CYP450 ), have been well elucidated ( Huang et al, 2021 ). In addition, structural genes of the flavonoid metabolic pathway are best understood at present ( Nabavi et al, 2020 ).…”

“…The recently published G. pentaphyllum genome sequence provides a convenient tool to identify and characterize the R2R3-GpMYB gene family ( Huang et al, 2021 ). In this study, we performed a genome-wide identification of R2R3-MYB genes in G. pentaphyllum and screened 87 R2R3-GpMYB genes.…”