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Background  Peppers ( Capsicum annuum  L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper.    Results  Here, we report de novo genome assemblies of  Capsicum annuum  ‘Early Calwonder (non-pungent, ECW)’ and ‘Small Fruit (pungent, SF)’ along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers.    Conclusions  Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in  Capsicum  species.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03057-8.

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper