Capsicum (Solanaceae) is a globally important vegetable crop and is also used therapeutically in traditional medicine systems. However, little is known of the genetic variation within the commonly grown cultivars, the evolutionary relationships and differences in the chloroplast (cp.) genomes between Capsicum species remain unclear. The cp. genomes of 32 Capsicum varieties in three species from 6 countries were investigated. The cp. genome of Capsicum was found to be ~ 156 kb in length and to contain 113 unique genes, of which 79 encoded proteins, 30 encoded transfer tRNAs, and 4 were for ribosomal RNAs. The 32 varieties that we chose for study represented 13 genotypes, containing a total of 608 indels, 83 SNPs, 47 SSRs and 281–306 repeat sequences. We then included several previously sequenced Capsicum cp. genomes, and found that the nine investigated species showed a number of differences in the characteristics of the four IR boundaries, and it was the non-coding regions that contained the most variable regions. We conducted a phylogenetic reconstruction using the cp. genomes of 43 representative species of Solanaceae, and the resulting phylogeny generally reflected the currently accepted classification, with the species of the pungent group having close relationship with one another. This study provides a comprehensive analysis of Capsicum chloroplast genomes, revealing significant variations in IR boundaries and other genomic features. These findings enhance our understanding of Capsicum evolution and genetic diversity.

Background: Capsaicinoid are a group of compounds and widely used in the food, medical, and pharmaceutical industries. Capsaicinoid are unique synthesized and accumulated in the pepper fruits. MeJA can enhance the capsaicinoid production. Temporal and spatial expression of capsaicinoid biosynthetic genes are helpful to understand the molecular mechnism of capsaicinoid biosynthesis in the fruits of pepper. Although some of the capsaicinoid biosynthetic genes in pepper have been identified, the expression of these genes at different developing stages of fruit has not been systemically investigated, and little is known about the molecular basis of MeJA inducing capsaicinoid biosynthesis. Results: HPLC study revealed that the capsaicinoid accumulation in the developing fruit of pepper initially appeared at 24 DAP (day after pollination), was actively development at 36 DAP and peaked at 48 DAP. 11 genes that encoded enzymes involved in capsaicinoid biosynthesis were isolated and characterized. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the CaCS was unique expressed in placenta and the other 10 genes were expressed in all selected tissues and 9 of 11 genes (except CaCa4H and CaCa3H) were strongly expressed in placenta tissue. Spatial expression analysis demostrated that the 11 gene could be collectively grouped into four categories based on the patterns of relative expression of the genes during fruit development. Category I has 2 and they displayed a bell-shaped expression pattern with the peak expression at 24 DAP, Category II contains 5 genes and expression of the 5 genes was constantly increased from 0 to 36 DAP and peaked at 36 DAP. Category III comprises of 2 genes and both genes reached the peak at 48 DAP. Category IV consists of 2 genes and they showed a high expression at 36 and 48 DAF, but unexpressed from 0 to 12 DAP. The gene expressions of the 11 genes were up-regulated by MeJA. 3 genes showed a high expression at 24 h; 4 genes reached the peak at 12 h; the top expression were observed at 18 h; The last one, CaACYase, achieved the highest level at 8 h. Conclusion: The biosynthesis of capsaicinoid in pepper fruit is developmentally regulated. The expression of the majority of capsaicinoid biosynthetic genes is highly consistent with the development accumulation of capsaicinoid in pepper fruit. These results not only provide the initial information on spatial and temporal expression of capsaicinoid biosynthetic genes in pepper developing fruit, but are also valuable to identify the MeJA-induced genes for capsaicinoid biosynthesis and accumulation during pepper fruit development.