Fig. 3: Convergent and divergent domestication of C. annuum var. annuum and C. baccatum var. pendulum.

a Fruits of representative wild and domesticated C. annuum and C. baccatum accessions with diverse shapes. Vertical bar represents 1 cm. b Fruit length, fruit width and fruit shape index in wild and domesticated C. annuum and C. baccatum accessions. Significant difference between groups was assessed using the two-tailed Student’s test. c, d Selective sweeps in C. annuum var. annuum (c) and C. baccatum var. pendulum (d). Fruit weight, shape, and pungency-related genes (in bold) and QTLs are presented in pink, orange, and cyan, respectively. Dashed horizontal lines indicate the top 5% Composite likelihood ratio (CLR) scores. Red dots correspond to selective sweeps identified in both C. annuum var. annuum and C. baccatum var. pendulum, and orange, dark green, dark orange and purple dots indicate CLR scores on different chromosomes. e Common and specific genome regions and genes under selection during C. annuum var. annuum and C. baccatum var. pendulum domestication. f, g Manhattan plots of genome-wide association studies of fruit shape of C. annuum (f) and C. baccatum (g) accessions. Red and blue horizontal lines indicate the Bonferroni-corrected significance thresholds of GWAS at α = 0.05 and α = 1, respectively. h Nucleotide diversity (π) and allele conservation of C. baccatum var. baccatum and C. baccatum var. pendulum accessions with fruit shape index >4 (the elongated dedo-de-moça type) and those with fruit shape index <1.2 (the cambuci type). GLA, C. annuum var. glabriusculum; ANN, C. annuum var. annuum; BAB, C. baccatum var. baccatum; BAP, C. baccatum var. pendulum. Detailed information on genes and QTLs is provided in Supplementary Data 6. Source data are provided as a Source Data file.