Multiple de novo Genome Sequences of Pepper Provide Insights into Species Diversification in Capsicum spp.

A diversity of Capsicum species has been derived from extensive genomic and phenotypic variations. Here, we report high-quality de novo genome sequences of two Capsicum species (C. chinense and C. baccatum) as multiple reference genomes of hot pepper. A total of 95 % of C. chinense (3.07 Gb of 3.21 Gb) and 76 % (3.22 Gb of 4.2 Gb) of C. baccatum genomes were assembled. Of these genome assemblies, 87.3 % (2.63 Gb) and 87.2 % (2.79 Gb) were anchored to 12 chromosome pseudomolecules, respectively. Comparative analysis with the existing pepper reference genome (C. annuum) revealed that the amount of ribosomal DNA sequences in C. baccatum was more than 10 fold compared to the other pepper genomes. Athila, a subgroup of Gypsy family, was excessively accumulated in C. baccatum and increased the genome size in this species compared to the others. Phylogenetic analysis revealed that speciation of C. baccatum and C. chinense from C. annuum had occurred at 1.7 and 1.1 million years ago, respectively. We identified correlations among proliferation of LTR retrotransposons, acceleration of gene expression change, gene duplication, and large genomic variations during the speciation of the pepper genomes. Our results support that rapid accumulation of LTR-retrotransposons during the speciation has contributed diversification of the three pepper genomes. The multiple pepper genomes will serve as important resources for comparative and population genomics as well as evolutionary studies of the genus Capsicum.