Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes

Abstract

Vitis adenoclada is a wild grape unique to China. It exhibits well resistance to heat, humidity, fungal disease, drought, and soil infertility. Here, we report the high-quality, chromosome-level genome assembly of GH6 (V. adenoclada). The 498.27 Mb genome contained 221.78 Mb of transposable elements, 28,660 protein-coding genes, and 481.44 Mb of sequences associated with 19 chromosomes. GH6 shares a common ancestor with PN40024 (Vitis vinifera) from approximately 4.26–9.01 million years ago, whose divergence occurred later than Vitis rotundifolia and Vitis riparia. Widely-targeted metabolome and transcriptome analysis revealed that the profiles and metabolism of phenolic compounds in V. adenoclada varieties significantly were differed from other grape varieties. Specifically, V. adenoclada varieties were rich in phenolic acids and flavonols, whereas the flavan-3-ol and anthocyanin content was lower compared with other varieties that have V. vinifera consanguinity in this study. In addition, ferulic acid and stilbenes content were associated with higher expressions of COMT and STSs in V. adenoclada varieties. Furthermore, MYB2, MYB73-1, and MYB73-2 were presumably responsible for the high expression level of COMT in V. adenoclada berries. MYB12 (MYBF1) was positively correlated with PAL, CHS, FLS and UFGT.Meanwhile, MYB4 and MYBC2-L1 may inhibit the synthesis of flavan-3-ols and anthocyanins in two V. adenoclada varieties (YN2 and GH6). The publication of the V. adenoclada grape genome provides a molecular foundation for further revealing its flavor and quality characteristics, is also important for identifying favorable genes of the East Asian species for future breeding.

Integrated non‐targeted metabolomics and transcriptomics reveals the browning mechanism of scraped ginger (Zingiber officinale Rosc.)

“…This led to differences in the expression of phenolic constituents. Phenolics serve as substrates in the enzymatic browning process (Wang et al., 2023c). The types and concentrations of phenolics exhibit significant variation across different organisms, leading to differences in the specific phenolics that play a major role in the browning process (Wang et al., 2023c).…”

“…Meanwhile, Wang et al. (2023c) employed integrated metabolomics to identify the browning substrates of apples, which encompass anthocyanins, tannins, erucic acid, and catechuic acid as their catalytic substrates. The study's findings demonstrated that within phenylpropanoid biosynthesis, phenolics such as chlorogenic acid and ferulic acid exhibit significant downregulation during the browning process of the scraped ginger.…”

Biography of Vitis genomics: recent advances and prospective

“…1 ). Studies on these genomes focused on grape berry quality (sugar, acid, aroma, pigment, and so on) [ 7 , 12 , 18 ], biotic and abiotic resistance [ 2 , 13 ], and future breeding strategies [ 9 , 22 ]. Through these genomes, researchers explored the mechanisms of disease resistance, high tannin content, and new breeding strategies.…”

“…Wild grape, which has high genetic diversity, has also been an important subject of grape genomic studies [ 10 , 13 , 18 ]. Wild Vitis species are widely found in the north of temperate zones and subtropics.…”

“…These species contain high genetic diversity and some unique genes that are non-existent in modern cultivars. Therefore, the exploration of key genes only existing in these wild species has also been a main task of grape research [ 9 , 10 , 13 , 18 , 23 ]. In 2020, the chromosome-level genome of V. amurensis , which is known as the most cold-resistant among Vitis species, was released.…”