Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.

The Clematis tangutica (Maxim.) Korsh. is a wild flowering plant that is most widely distributed on the Qinghai–Tibet Plateau, with beautiful, brightly colored flowers and good ornamental properties and adaptability. In diverse natural environments, the blossom color of C. tangutica (Maxim.) Korsh. varies greatly, although it is unclear what causes this diversity. It was examined using UPLC-MS/MS and transcriptome sequencing for the investigation of various compounds, differentially expressed genes (DEGs), and flavonoid biosynthesis-related pathways in two flowers in two ecological settings. The results showed that a total of 992 metabolites were detected, of which 425 were differential metabolites, mainly flavonoid metabolites associated with its floral color. The most abundant flavonoids, flavonols and anthocyanin metabolites in the G type were cynaroside, isoquercitrin and peonidin-3-O-glucoside, respectively. Flavonoids that differed in multiplicity in G type and N type were rhoifolin, naringin, delphinidin-3-O-rutinoside, chrysoeriol and catechin. Rhoifolin and chrysoeriol, produced in flavone and flavonol biosynthesis, two flavonoid compounds of C. tangutica (Maxim.) Korsh. with the largest difference in floral composition in two ecological environments. In two ecological environments of flower color components, combined transcriptome and metabolome analyses revealed that BZ1-1 and FG3-1 are key genes for delphinidin-3-O-rutinoside in anthocyanin biosynthesis, and HCT-5 and FG3-3 are key genes for rhoifolin and naringin in flavonoid biosynthesis and flavone and flavonol. Key genes for chlorogenic acid in flavonoid biosynthesis include HCT-6, CHS-1 and IF7MAT-1. In summary, differences in flavonoids and their content are the main factors responsible for the differences in the floral color composition of C. tangutica (Maxim.) Korsh. in the two ecological environments, and are associated with differential expression of genes related to flavonoid synthesis.

Jerusalem artichoke (Helianthus tuberosus L.) reproduces asexually through tubers, which are rich in fructan-type carbohydrates and serve as the primary processing organ. Plant hormones may regulate the sprouting process of tubers, but the changes in fructans and their regulatory mechanisms in relation to hormones remain unclear. This study utilized two varieties of Jerusalem artichoke, “Qingyu No.1” and “Qingyu No.3”, to analyze the changes in the proportion of carbohydrates (especially fructans) in total sugars during the sprouting process. Metabolomic and transcriptomic analyses were conducted at three selected sprouting stages. The results indicated that during tuber sprouting, carbohydrates such as fructans play a regulatory role through conversion activities. Multi-omics analysis revealed that jasmonic acid and salicylic acid promote Jerusalem artichoke sprouting through metabolism and are involved in the plant hormone signal transduction process. Differentially expressed genes related to hormone signaling were screened and divided into three groups based on expression levels. It was found that the proportion of carbohydrates is highly correlated with the expression of hormone-related genes in the sprouts, suggesting that plant hormones may regulate carbohydrate metabolism during the sprouting of Jerusalem artichoke tubers. In conclusion, these results preliminarily elucidate the regulatory mechanisms of plant hormones in Jerusalem artichoke tuber sprouting, aiming to provide a theoretical basis for the production and processing of Jerusalem artichoke.

Purpose Chicory is consumed worldwide and is an important commercial crop. However, excess lignin deposition may reduce its quality. The molecular mechanisms underlying lignin remain poorly understood. To address this, an integrative analysis of the metabolome and transcriptome profiles was performed in chicory sprout at 3 different stages.Methods In this study, metabolites of the lignin biosynthesis pathway in chicory growth were determined by UPLC-MS/MS, moreover, multi-group sequencing and quantitative analysis of the transcriptome.Results A total of 706 metabolites were identified, with cinnamic acid, ferulic acid, Coniferaldehyde, and sinapaldehyde enriched during the growth of chicory sprouts. This suggested that these four metabolites may affect the growth of chicory sprouts. Transcriptome analysis demonstrated the expression of most of the differentially expressed genes (DEGs) involved in lignin biosynthesis was up-regulated during chicory growth.Conclusion Importantly, the metabolite and gene expression profiles were closely correlated during sprout development, especially in association with lignin biosynthesis. The results will serve as a reference for lignin biosynthesis in chicory and may also assist biologists in improving chicory quality.