Carotenoids are important pigments in pepper fruits. The colors of each pepper are mainly determined by the composition and content of carotenoid. The ‘ZY’ variety, which has yellow fruit, is a natural mutant derived from a branch mutant of ‘ZR’ with different colors. ZY and ZR exhibit obvious differences in fruit color, but no other obvious differences in other traits. To investigate the main reasons for the formation of different colored pepper fruits, transcriptome and metabolome analyses were performed in three developmental stages (S1–S3) in two cultivars. The results revealed that these structural genes (PSY1, CRTISO, CCD1, CYP97C1, VDE1, CCS, NCED1 and NCED2) related to carotenoid biosynthesis were expressed differentially in the two cultivars. Capsanthin and capsorubin mainly accumulated in ZR and were almost non-existent in ZY. S2 is the fruit color-changing stage; this may be a critical period for the development of different color formation of ZY and ZR. A combination of transcriptome and metabolome analyses indicated that CCS, NCED2, AAO4, VDE1 and CYP97C1 genes were key to the differences in the total carotenoid content. These new insights into pepper fruit coloration may help to improve fruit breeding strategies.

Fruit color serves as a crucial visual indicator in chili peppers and is closely linked to the bioactive components that determine their economic and nutritional value. However, the specific components and potential molecular mechanisms that impact fruits’ development and color changes are less thoroughly understood. Here, we utilized three chili pepper varieties (CS03, CS29, and L816) at different developmental stages (young fruit stage, turning color stage, and mature stage) as research materials and integrated transcriptome and non-targeted metabolome analyses to explore the variation in bioactive components and color to explain the molecular regulatory mechanisms underlying different colors of chili peppers during the young fruit stage. Our results showed that flavonoids were the most enriched differential metabolites; aromadendrin 4′-glucoside, diospyrin, precarthamin, kaempferol-3-O-rutinoside, and kaempferol-3-O-Glucoside were significantly enriched in the young fruit stage of pepper CS03; and cyanidin, delphinidin, and cyanidin 3-glucoside were major contributors to the color formation. The upregulation of anthocyanin was related to the structural genes CaC4H, Ca4CL, CaCHS, CaF3H, CaANS, and CaUFGT, and key transcription factors such as CaMYBs and CabHLHs may have contributed to the differential accumulation of anthocyanins in CS03; in addition, RT-qPCR validation was correlated with anthocyanins, but also with flavonoids. This article mainly focuses on the changes in chili pigments, particularly anthocyanins, and explores the molecular mechanisms involved. This provides a reference for research on color in solanaceae vegetables and lays a theoretical foundation for further research on the bioactive components of chili peppers, as well as for optimizing harvesting practices and dietary recommendations.

Anthocyanins are important flavonoid compounds in plants that are associated with the color formation and antioxidant activity of flowers, fruits, and other organs. Ultraviolet B radiation (UV-B) is one of the key environmental factors that influence anthocyanin accumulation in plants and HY5 is involved in plant photomorphogenesis. However, the molecular mechanism of the signal network of UV-B regulating anthocyanin biosynthesis in capsicum via HY5 remains unclear. In this study, we identified the transcription factor CaHY5, which mediates UV-B signaling, and demonstrated its regulatory role in anthocyanin biosynthesis in purple pepper (Capsicum annuum L.). The results showed that there were photoresponsive and hormone-responsive elements on the CaHY5 promoter that responded to UV-B, indoleacetic acid, salicylic acid, 6-benzyladenine, abscisic acid, and melatonin treatments. UV-B treatment induced the expression of CaHY5 and anthocyanin structural genes. CaHY5 gene-silenced positive plants showed different degrees of the yellowing phenomenon, which affected the expression of the anthocyanin biosynthesis structural gene. The expression levels of anthocyanin biosynthesis-related genes in CaHY5-silenced positive plants increased considerably. This study provides insights into the role of CaHY5 in UV-B-induced anthocyanin biosynthesis in purple pepper.

An in-house tomato inbred line, YNAU335, was planted in a greenhouse in spring from 2014 to 2017, and showed immunity to tomato spotted wilt virus (TSWV). YNAU335 was infected with TSWV in the spring from 2018 to 2020, and disease was observed on the leaves, sepals, and fruits. In 2021 and 2022, YNAU335 was planted in spring in the same greenhouse, which was suspected of being infected with TSWV, and visible disease symptoms were observed on the fruits. Transmission electron microscopy, deep sequencing of small RNAs, and molecular mutation diagnosis were used to analyze the pathological features and genetic polymorphism of TSWV infecting tomato fruit. Typical TSWV virions were observed in the infected fruits, but not leaves from YNAU335 grown between 2021 and 2022, and cross-infection was very rarely observed. The number of mitochondria and chloroplasts increased, but the damage to the mitochondria was greater than that seen in the chloroplasts. Small RNA deep sequencing revealed the presence of multiple viral species in TSWV-infected and non-infected tomato samples grown between 2014–2022. Many virus species, including TSWV, which accounted for the largest proportion, were detected in the TSWV-infected tomato leaves and fruit. However, a variety of viruses other than TSWV were also detected in the non-infected tissues. The amino acids of TSWV nucleocapsid proteins (NPs) and movement proteins (MPs) from diseased fruits of YNAU335 picked in 2021–2022 were found to be very diverse. Compared with previously identified NPs and MPs from TSWV isolates, those found in this study could be divided into three types: non-resistance-breaking, resistance-breaking, and other isolates. The number of positive clones and a comparison with previously identified amino acid mutations suggested that mutation F at AA118 of the MP (GenBank OL310707) is likely the key to breaking the resistance to TSWV, and this mutation developed only in the infected fruit of YNAU335 grown in 2021 and 2022.

The homeodomain–leucine zipper (HD-zip) gene family plays a crucial role in plant development and stress responses. However, systematic identification studies of this gene family in eggplant are still lacking. In this study, we systematically identified 44 HD-zip genes in the eggplant genome database using bioinformatics methods and analyzed their expression levels under light and multiple hormones by RT-qPCR. The results show that members of the SmHD-zip gene family were classified into four groups (HD-zip I, II, III, and IV) based on the phylogenetic relationship. Cis-acting elements related to plant development, hormones, and stress were identified in the promoter regions of the SmHD-zip gene family. Furthermore, the expression of the SmHDZ2 gene was upregulated during the fruit development stage, while nine SmHD-zip genes exhibited downregulated expression patterns. Notably, some SmHD-zip genes were identified as key regulators of eggplant responses to light and multiple hormone signals. Overall, these findings not only provide valuable insights into the evolutionary and functional characteristics of eggplant HD-Zips but also suggest that HD-zip genes likely play a significant role in regulating fruit development and ripening by integrating light and multiple hormone signaling pathways. Therefore, this study laid the foundation for further research on eggplant quality.