Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

Abstract

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.

Keywords: Solanaceae evolution; de novo genome sequence; genome expansion.

Fig. 1.

Global view of the pepper genome. Track A denotes the 12 pseudochromosomes of pepper (megabases). The positions of the effective markers in the genetic map are shown as vertical gray lines. The loci of inferred centromeres are denoted by vertical red bars. Track B shows density of recombination. Track C shows density distribution of Gypsy (green), Copia (light blue), and protein-coding genes (navy). Track D shows distribution of tissue-specific expression genes, including root (red), stem (green), leaf (dark magenta), flower (blue), and fruit (gold). Track E shows genome-wide distribution of total small RNA loci (blue and green lines). The histograms plot small RNA reads from 20 to 25 nt, and they were normalized to account for the appearance of opposite strand inverse sequences. Track F shows distribution of the identified miRNA families denoted by different colors (Dataset S6). Track G shows connections of the triplicate loci denoted by different colors (Dataset S16).

Fig. 2.

Comparative analysis and evolution of the pepper genome. (A) Genomic differences among C. annuum, Solanum lycopersicum, Solanum tuberosum, Arabidopsis thaliana, Carica papaya, Vitis vinifera, and Oryza sativa. Neighbor-joining phylogenetic analysis was performed with orthologous genes and all coding DNA sequence (CDS) in C. annuum and the other six plants. (B) Clusters of orthologous and paralogous gene families in the seven plant species identified by OrthoMCL. (C) Syntenic blocks in the cultivated pepper, tomato, and potato show that genome rearrangements have occurred among these taxa. (D) Genome duplication in dicot genomes (pepper, tomato, potato, and grape) revealed by 4DTv analyses.

Fig. 3.

Diversity in domesticated pepper population. (A) Diversity metrics (θ_π, θ_w, and Tajima D) are shown for 19 domesticated varieties across Chr03, -09, and -11. (B) Illustration of the strategy for candidate selection regions. The gray region above the x axis corresponds to regions with 0.5% significance level of diversity difference.

Fig. 4.

Putative acyltransferase (AT3) genes for pungency and gene expression patterns of selected tissues and genes. (A) Phylogenetic analysis of the AT3 gene family among Zunla-1, Chiltepin, Arabidopsis, potato, and tomato. (B) The comparison of AT3 protein sequences among pepper, tomato, and potato. The nucleotide similarity of these proteins is shown in Upper, and the alignment is shown in Lower. The aligned codon sequences of an amino acid with zero, one, and two mutants among pepper, tomato and potato are marked by “*”, “.”, and “:”, respectively. (C) The concentrations of capsaicin and dihydrocapsaicin, gene expression patterns in selected tissues of Capsicum species, and genes involved in capsaicin synthesis are shown. The green background denotes secondary metabolites (capsaicin and dihydrocapsaicin), and the red background indicates genes that are expressed in selected tissues of Capsicum species. RPKM, reads per kb per million mapped reads. Additionally, the gray background indicates missing data. Zunla-1, Chiltepin, HYL, JZ32, and G16 are pungent peppers; SP163, T803, 11c320, ZJ9, and 11c255 are nonpungent peppers. A model of capsaicin synthesis illustrating secondary metabolite and genes encoding enzymes is showed in SI Appendix, Fig. S15. Full names of genes encoding enzymes are shown in Dataset S26.