Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

辣椒（ Capsicum ）因其含有类辣椒素而具有独特的水果辛辣味而闻名。由于缺乏高质量的辣椒基因组，辣椒素生物合成的进化史及其组织特异性的机制仍然不清楚。在这里，我们报告了C. annuum及其野生无刺激性亲戚C. rhomboideum的两个端粒到端粒（T2T）无间隙基因组，以研究辣椒中水果辛辣味的进化。我们精确地描绘了辣椒着丝粒，该着丝粒缺乏高拷贝串联重复序列，但被 CRM 反转录转座子广泛入侵。通过系统发育分析，我们估计了辣椒素生物合成的进化时间。我们揭示了非刺激性物种中关键生物合成基因的编码和调控区域被破坏。我们还发现了保守的胎盘特异性可及染色质区域，这可能允许组织特异性生物合成基因共调节和辣椒素积累。这些T2T基因组资源将加速辣椒遗传改良，并有助于了解辣椒基因组进化。