Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
Nat Commun. 2024 May 20;15(1):4295. doi: 10.1038/s41467-024-48643-0.
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）因其果实的独特辣味而闻名，这种辣味是由于存在辣椒素类物质。由于缺乏高质量的辣椒基因组，辣椒素生物合成的进化历史及其组织特异性的机制仍不清楚。在这里，我们报告了两个端粒到端粒（T2T）无间隙的 C. annuum 和其野生非辣味近缘种 C. rhomboideum 的基因组，以研究辣椒果实辣味的进化。我们精确地描绘了辣椒的着丝粒，着丝粒缺乏高拷贝串联重复序列，但广泛被 CRM 反转录转座子入侵。通过系统基因组学分析，我们估计了辣椒素生物合成的进化时间。我们揭示了非辣味物种中关键生物合成基因的编码和调控区的中断。我们还发现了保守的胎盘特异性可及染色质区域，这些区域可能允许组织特异性生物合成基因的共调控和辣椒素的积累。这些 T2T 基因组资源将加速辣椒的遗传改良，并有助于理解辣椒基因组的进化。
