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Limited knowledge is available for phosphorylation modifications in pepper (Capsicum annuum L.), especially in pepper fruit development. In this study, we conducted the first comprehensive phosphoproteomic analysis of pepper fruit at four development stage by Tandem Mass Tag proteomic approaches. A total of 2639 unique phosphopeptides spanning 1566 proteins with 4150 nonredundant sites of phosphorylation were identified, among which 2327 peptides in 1413 proteins were accurately quantified at four different stages. Mature Green (MG) to breaker stage showed the largest number of differentially expressed phosphoproteins and the number of downregulated phosphoproteins was significantly higher than that of upregulated after MG stage. Twenty seven phosphorylation motifs, including 22 pSer motifs and five pThr motifs and 85 kinase including 28 serine/threonine kinases, 14 receptor protein kinases, six mitogen-activated protein kinases, seven calcium-dependent protein kinases, two casein kinases, and some other kinases were quantified. Then the dynamic changes of phosphorylated proteins in ethylene and abscisic acid signaling transduction pathways during fruit development were analyzed. Our results provide a cascade of phosphoproteins and a regulatory network of phosphorylation signals, which help to further understand the mechanism of phosphorylation in pepper fruit development. [ABSTRACT FROM AUTHOR]

• It was first identified that CaSRM1 controls leaf shape change in pepper. • CaSRM1 has functional differentiation compared with SRM1 genes in other crops. • The leaf changes of CaSRM1 overexpression and silencing lines relation cell division. • CaSRM1 depends on the auxin pathway and affects the other leaf-shaped genes. • CaSRM1 showed potential in regulating fruit shape development. Pepper is among the most economically important solanaceous vegetable crops worldwide. The shape and spatial distribution of leaves affect the light energy use efficiency of the plant, which strongly affects the yield and quality of pepper fruit. However, the molecular mechanisms underlying pepper leaf development are unknown. In this study, we demonstrated that the CaSRM1 gene regulates pepper leaf morphology. Virus-induced gene silencing was used to reveal that silencing of CaSRM1 caused development of uneven leaf margins and curling of pepper leaves. Overexpression of CaSRM1 in tomato led to leaf morphological defects, but was accompanied by improved vegetative growth and larger fruit. The expression level of CaSRM1 in mature tissues was higher than that in young tissues of pepper plant, and its expression was induced by auxin. Analysis of phytohormone contents and expression of leaf shape-related genes revealed that the auxin content showed an opposite trend to CaSRM1 expression, and certain leaf shape-related genes were affected by CaSRM1 expression, especially auxin-related genes. The results provide important information for functional research on other SRM1 genes and offer a novel perspective to the mechanism of plant leaf and fruit development. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are non-coding small RNAs which play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are involved in fruit development in model plants. However, the miRNAs related to fruit development and quality in hot pepper ( Capsicum annuum L.) remains unknown. In this study, small RNA populations from different fruit ripening stages and different varieties were compared using next-generation sequencing technology. Totally, 59 known miRNAs and 310 novel miRNAs were identified from four libraries using miRDeep2 software. For these novel miRNAs, 656 targets were predicted and 402 of them were annotated. GO analysis and KEGG pathways suggested that some of the predicted miRNAs targeted genes involved in starch sucrose metabolism and amino sugar as well as nucleotide sugar metabolism. Quantitative RT-PCR validated the contrasting expression patterns between several miRNAs and their target genes. These results will provide an important foundation for future studies on the regulation of miRNAs involved in fruit development and quality. [ABSTRACT FROM AUTHOR]