Multiple Reference Genomes of Hot Pepper Reveal the Massive Evolution of Plant Disease Resistance Genes By Retroduplication

Transposons are one of the major evolutionary forces leading to new gene sequences and ultimately species diversification. However, the mechanisms by which transposons contribute to the evolution of the immune system are largely unexplored in plants. Here, we report high-quality de novo genomes of two peppers (C. baccatum PBC81 and C. chinense PI159236) and the improved reference genome. Dynamic genome rearrangements were derived from translocation among chromosome 3, 5 and 9 between C. baccatum and the other peppers. Evolution analyses of LTR-retrotransposons indicated that exclusive accumulation of athila subgroup of gypsy family have led to genome expansion of C. baccatum. In-depth genome-wide comparison of genes and repeats of peppers unveiled that copy numbers of NLRs belonging to specific subgroups (CNL-G2) were excessively increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs have generally existed and species-specifically expanded in plants. Our study revealed that retroduplication has played a key role for the emergence of functional disease resistance genes in Solanaceae family.