Genome sequences and annotation files of two hermaphrodite Cara papaya varieties: Kamiya and Suizhonghong

Genome assemblies and annotations files of 'KamiyaQ8' common-type 'SuizhonghongQ1'. We successfully assembled the genomes of two hermaphroditic papaya cultivars with XYh sexual type (a fruit-type ‘Kamiya’ cultivated for fresh use and a common-type ‘Suizhonghong’ cultivated for vegetable use) using a combination of sequencing technologies, including long-read PacBio, high-throughput chromosome conformation capture (Hi-C), and short-read Illumina. We rebuilt the X-linked regions and hermaphrodite-specific Yh counterparts (HSY) within the sex-determining regions (SDRs) of the ‘Kamiya’ and ‘Suizhonghong’ varieties. The X-region of ‘Kamiya’ spanned 5.42 Mb and contained 192 protein-coding genes, while the HSY-region was 9.37 Mb and harbored 283 protein-coding genes. The X-region of ‘Suizhonghong’ covered 5.56 Mb and housed 196 protein-coding genes, while the HSY-region spanned 9.34 Mb and had 243 protein-coding genes.