Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

Abstract Chili pepper (Capsicum), one of oldest domesticated crops in human history, is best known for its unique fruit pungency given by capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of tissue-specificity remain obscured due to the lack of high-quality Capsicum genomes. Here, we assembled two telomere-to-telomere (T2T) gap-free genomes for C. annuum and its wild non-pungent relative C. rhomboideum to dissect the evolution of fruit pungency in chili peppers. We precisely delineated Capsicum centromeres which, unlike Arabidopsis and human centromeres, lacked high-copy centromeric tandem repeats but were extensively invaded by CRM LTR retrotransposons. Phylogenomics estimated the evolutionary timings of capsaicinoid biosynthesis, and revealed eroded coding and regulatory regions of key biosynthesis genes in non-pungent species such as C. rhomboideum. We also found conserved placenta-specific accessible chromatin regions likely allowing tissue-specific biosynthesis gene co-regulation. Finally, from detected copy number variants of capsaicinoid biosynthesis genes using the C. annuum T2T genome as reference, we trained a machine-learning model to predict pungency for genomic selection. The new T2T genomic resources will accelerate chili pepper breeding, metabolic engineering and enrich our understanding of Capsicum biology and genome evolution.