Capsicum frutescens is a valuable economic crop that is widely cultivated for its unique flavor and rich nutritional content. While some studies have shown differences in flavonoid content among different chili species, the mechanism by which changes in flavonoid composition lead to fruit color variations in C. frutescens remains underreported. We performed transcriptomics and widely targeted metabolome sequencing on three different growth stages of the C. frutescens fruit and analyzed the data to better understand the mechanism of color change. Based on previous research on the genes that regulate flavonoid compounds and the MBW complex, we have identified a total of 28 core genes related to flavonoid biosynthesis and 8 genes that may be related to flavonoid synthesis. Through extensive targeted metabolomic analysis, 581 differential metabolites were identified, including 43 flavonoids. Most anthocyanins, flavonols, and flavonoids were found to be more abundant during the immature fruit stage, which we presume is associated with the differential expression of genes involved in flavonoid biosynthesis and regulation. These findings provide a useful reference for understanding flavonoid synthesis and the accumulation of fruits in C. frutescens.

Introduction: Solanum nigrum , a member of the Solanaceae family, holds significant importance in various aspects, including edible and medicinal uses, ecological management, and environmental landscaping. The leaf edges of S. nigrum exhibit 4–5 significant serrations, and the splitting of these leaf margins plays a crucial role in the plant’s adaptation to environmental shifts. Methods: In this study, we systematically analyzed the molecular mechanism of leaf margin fission in S. nigrum by combining RNA sequencing, weighted gene co-expression network analysis, and overexpression transgenic technology using leaves from five growth stages of S. nigrum during the flowering period as materials. Results: Transcriptome analysis revealed that 30,311 differentially expressed genes were activated from leaf bud to mature leaf, and these genes were significantly enriched in metabolic pathways related to signal transduction and glycosynthesis. Differential genes were hierarchically clustered into 13 modules. The correlations of these modules with different growth stages of S. nigrum leaves, as well as the number and depth of leaf notches were analyzed. It was found that the turquoise expression module (ME1) was significantly and positively correlated with the leaf bud stage (r = 0.94, p < 0.01), while negatively correlated with the number and depth of leaf notches. Three highly connected hub genes were identified from network interactions analysis of genes related to the leaf differentiation pathway in Module 1. From the intersection of the turquoise module and the 2 clusters screened by temporal analysis, the core gene ( SnNAC90 ) for leaf margin fission in lobelia was identified. The regulatory role of the SnNAC90 gene in tobacco leaves was preliminarily verified by transgenic technology. Discussion: It was hypothesized that it might positively regulate leaf margin fission in S. nigrum . Preliminary speculation on its regulatory role in S. nigrum leaves. This study, for the first time, revealed the regulatory mechanism of leaf margin division in S. nigrum , providing a theoretical basis for enriching its germplasm resources and serving as a reference basis for cultivating leaf plants.

Capsicum baccatum is a close relative of edible chili peppers (Capsicum annuum) with high economic value. The CBF gene family plays an important role in plant stress resistance physiology. We detected a total of five CBF genes in the C. baccatum genome-wide sequencing data. These genes were scattered irregularly across four chromosomes. The genes were categorized into three groupings according to their evolutionary relationships, with genes in the same category showing comparable principles for motif composition. The 2000 bp upstream of CbCBF contains many resistance-responsive elements, hormone-responsive elements, and transcription factor binding sites. These findings emphasize the crucial functions of these genes in responding to challenging conditions and physiological regulation. Analysis of tissue-specific expression revealed that CbCBF3 exhibited the greatest level of expression among all tissues. Under conditions of low-temperature stress, all CbCBF genes exhibited different levels of responsiveness, with CbCBF3 showing a considerable up-regulation after 0.25 h of cold stress, indicating a high sensitivity to low-temperature response. The importance of the CbCBF3 gene in the cold response of C. baccatum was confirmed by the use of virus-induced gene silencing (VIGS) technology, as well as the prediction of its protein interaction network. To summarize, this study conducts a thorough bioinformatics investigation of the CbCBF gene family, showcases the practicality of employing VIGS technology in C. baccatum, and confirms the significance of the CbCBF3 gene in response to low temperatures. These findings provide significant references for future research on the adaptation of C. baccatum to low temperatures.