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A diversity of Capsicum species has been derived from extensive genomic and phenotypic variations.Here, we report high-quality de novo genome sequences of two Capsicum species (C.chinense and C.baccatum) as multiple reference genomes of hot pepper.A total of 95 % of C.chinense (3.07 Gb of 3.21 Gb) and 76 % (3.22 Gb of 4.2 Gb) of C.baccatum genomes were assembled.Of these genome assemblies, 87.3 % (2.63 Gb) and 87.2 % (2.79 Gb)were anchored to 12 chromosome pseudomolecules, respectively.