Transcriptomic and Metabolomic Analyses Providing Insights into the Coloring Mechanism of Docynia delavayi

Biodiversity and Winemaking Characteristics of Yeasts Isolated from Docynia delavayi (Franch.) Schneid. Wine Microbiota

The community of epibiotic yeasts significantly influences the quality of Docynia delavayi (Franch.) Schneid. wine. The yeast diversity in four different Docynia delavayi (Franch.) Schneid. wines during the brewing stage was investigated using pure culture methods and high-throughput sequencing technology. A total of 229,381,292 sequencing bases were generated, yielding 323,820 valid sequences with an average length of 708 nt and identifying 93 operational taxonomic units (OTUs) from naturally fermented samples of Docynia delavayi (Franch.) Schneid. wine for classification purposes. At the early fermentation stage, Hanseniaspora sp. was identified as the dominant species, whereas at the late fermentation stage, Hanseniaspora sp., Saccharomyces sp., and Candida californica became predominant. From these samples, a total of 109 yeast strains were isolated from Docynia delavayi (Franch.) Schneid. wine. Three specific strains-LZX-76, LZX-89, and LZX-104-were further selected based on their growth characteristics along with hydrogen sulfide production, ester production, ethanol production, and tolerance levels. Through morphological examination and molecular biology techniques, these strains were identified as Pichia fermentans and Hanseniaspora spp. Additionally, a total of 29 volatile compounds were detected through simulated fermentation processes; these included 12 esters, 6 alcohols, 2 acids, 4 aldehydes, and 5 other compounds. When compared to commercial yeasts used as starters in winemaking processes, it was observed that utilizing yeast strains LZX-76, LZX-89, and LZX-104 resulted in an increased number of volatile compounds, which enhanced the aromatic profile characteristics of Docynia delavayi (Franch.) Schneid. wine by making its aroma richer and more complex. The findings from this study hold significant potential value for both the production practices and research endeavors related to Docynia delavayi (Franch.) Schneid. wine.

Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica

The color of coffee fruits is influenced by several factors, including cultivar, ripening stage, and metabolite composition. However, the metabolic accumulation of pigments and the molecular mechanisms underlying peel coloration during the ripening process of Coffea arabica L. remain relatively understudied. In this study, UPLC-MS/MS-based metabolomics and RNA sequencing (RNA-seq)-based transcriptomics were integrated to investigate the accumulation of anthocyanins and carotenoids in the peel of Coffea arabica at different ripening stages: green peel (GP), green-yellow peel (GYRP), red peel (RP), and red-purple peel (RPP). This integration aimed at elucidating the molecular mechanisms associated with these changes. A total of ten anthocyanins, six carotenoids, and thirty-five xanthophylls were identified throughout the ripening process. The results demonstrated a gradual decrease in the total carotenoid content in the peel with fruit maturation, while anthocyanin content increased significantly. Notably, the accumulation of specific anthocyanins was closely associated with the transition of peel colors from green to red. Integrated metabolomics and transcriptomics analyses identified the GYRP stage as critical for this color transition. A weighted gene co-expression network analysis (WGCNA) revealed that enzyme-coding genes such as 3AT, BZ1, and lcyE, along with transcription factors including MYB, NAC, and bHLH, which interact with PHD and SET TR, may regulate the biosynthesis of anthocyanins and carotenoids, thereby influencing peel pigmentation. These findings provide valuable insights into the molecular mechanisms underlying the accumulation of anthocyanins and carotenoids in Coffea arabica peel during fruit maturation.

Chromosome-scale genome assembly of Docynia delavayi provides new insights into the α-farnesene biosynthesis

Docynia delavayi is an economically significant fruit species with a high market potential due to the special aroma of its fruit. Here, a 653.34 Mb high-quality genome of D. delavayi was first reported, of which 93.8 % of the sequences (612.98 Mb) could be anchored to 17 chromosomes, containing 48,325 protein-coding genes. Ks analysis proved that two whole genome duplication (WGD) events occurred in D. delavayi, resulting in the expansion of genes associated with terpene biosynthesis, which promoted its fruit-specific aroma production. Combined multi-omics analysis, α-farnesene was detected as the most abundant aroma substance emitted by D. delavayi fruit during storage, meanwhile one α-farnesene synthase gene (AFS) and 15 transcription factors (TFs) were identified as the candidate genes potentially involved in α-farnesene biosynthesis. Further studies for the regulation network of α-farnesene biosynthesis revealed that DdebHLH, DdeERF1 and DdeMYB could activate the transcription of DdeAFS. To our knowledge, it is the first report that MYB TF plays a regulatory role in α-farnesene biosynthesis, which will greatly facilitate future breeding programs for D. delavayi.

Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review

Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.

Anthocyanins in metabolites of purple corn

Purple corn (Zea mays L.) is a special variety of corn, rich in a large amount of anthocyanins and other functional phytochemicals, and has always ranked high in the economic benefits of the corn industry. However, most studies on the stability of agronomic traits and the interaction between genotype and environment in cereal crops focus on yield. In order to further study the accumulation and stability of special anthocyanins in the growth process of purple corn, this review starts with the elucidation of anthocyanins in purple corn, the biosynthesis process and the gene regulation mechanism behind them, points out the influence of anthocyanin metabolism on anthocyanin metabolism, and introduces the influence of environmental factors on anthocyanin accumulation in detail, so as to promote the multi-field production of purple corn, encourage the development of color corn industry and provide new opportunities for corn breeders and growers.

Analyzing Volatile Compounds of Young and Mature Docynia delavayi Fruit by HS-SPME-GC-MS and rOAV

This study focused on the examination of the volatile compounds and fragrance properties of the young and mature fruit of Docynia delavayi. Headspace solid-phase microextraction combined with gas chromatography−mass spectrometry (HS-SPME-GC-MS) was applied for identifying 42 volatile compounds, with young and mature fruit containing 36 and 42 compounds, respectively. Heat map cluster analysis, principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and independent sample t-testing were used to analyze sample differences. Based on a variable importance in projection (VIP) > 1 and p < 0.05, 23 key volatile compounds such as octanal, geranylacetone, butyl acetate, and dihydro-β-ionone were screened. β-Ionone and phenethyl acetate made the largest contribution to the aroma of D. delavayi after analyzing the relative odor activity value (rOAV) of the key volatile compounds and their aroma descriptors. Young D. delavayi fruit exhibited a prominent woody scent, while mature D. delavayi fruit had more intense floral and rosy aromas. The findings may lay a foundation for comprehensively developing and utilizing D. delavayi fruit.