de novo Sequencing and Analysis of Multiple Pepper Genomes Provide Insight into the Evolution of Capsicum spp

A diversity of Capsicum species has been derived from extensive genomic and phenotypic variations. Here, we report high-quality de novo genome sequence of two Capsicum species (Capsicum chinense and Capsicum baccatum) and comparative analysis with completed genome sequences of Solanaceae species including existing pepper reference genome. We identified that the disease resistance genes were exclusively expanded in Capsicum species by tandem duplication compared to other Solanaceae genomes. The phylogenetic analysis revealed speciation time between Solanaceae and Capsicum species and among Capsicum species. Overall, the transposable elements (TEs) covered over 70 % of three pepper genomes and the long terminal repeats (LTRs) occupied the major proportion. Even though similar amount of LTRs was accumulated in each pepper genome, the distribution of LTRs insertion time showed that the accumulation of LTRs for C. chinense and C. baccatum were distinctly increased around the speciation time. Our analyses unveiled large and small genomic variations contributing divergence of the three pepper genomes. The multiple pepper genomes will serve as versatile references for population genomics and breeding in Capsicum spp.