Two T2T Pepper Genomes Reveal How Capsaicinoid Pungency Evolved and Became Placenta-Specific

A 2024 Nature Communications study assembled telomere-to-telomere, gap-free genomes for pungent Capsicum annuum and its nonpungent wild relative C. rhomboideum to examine the evolution and tissue specificity of capsaicinoid biosynthesis.

Gap-free genomes for repeat-rich Capsicum

Pepper genomes are roughly 3 Gb and ~80% repetitive, making complete assembly difficult. The new T2T resources support detailed comparison of centromeres, gene duplications and regulatory regions.

Capsaicinoid biosynthesis evolved through pathway assembly and gene regulation

Capsaicinoids combine precursors from phenylpropanoid and branched-chain fatty-acid metabolism through capsaicin synthase-related activity. Phylogenomics helps reconstruct duplication and loss of pathway components, but the authors emphasize that too few high-quality genomes exist across the >40 Capsicum species to completely resolve every evolutionary step.

Placenta-specific open chromatin helps localize pungency

RNA-seq, ATAC-seq and methylation profiling identified placenta-associated open chromatin around CS-2 and regulators such as MYB31 and MYB48. Nonpungent C. annuum accessions carried a 2.4-kb deletion affecting the CS-2 upstream open-chromatin region.

Thus pungency depends not only on coding genes but also on when and where the pathway is accessible and expressed.

The genomes are valuable breeding and engineering resources, but they do not yet provide a simple recipe for designing any desired capsaicinoid level.

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Reference

• Chen W et al. Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis. Nature Communications. 2024;15:4295. https://doi.org/10.1038/s41467-024-48643-0