A draft genome assembly and resequencing analysis of Chinese cherry (Cerasus pseudocerasus) reveal structural variants associated with fruit traits

Chinese cherry (Cerasus pseudocerasus) is a significant fruit crop that enjoys widespread cultivation in China. Here, we report a draft autotetraploid genome assembly of the Chinese cherry cultivar ‘Huangguo’, characterized by a size of 340.99 Mb and comprised of 261,760 contig sequences. We further obtained resequencing data of eight Chinese cherry varieties, with an average sequencing depth of approximately 57 × per individual. Population structure analysis revealed that the eight varieties were partitioned into two distinct groups. Additionally, the genetic relationship matrix analysis indicated that ‘Changbing’ and ‘Duanbing’ shared the closest genetic background. Moreover, we have creatively established a workflow for transforming heterozygous genotypes from diploid format to tetraploid format by conducting secondary genotyping in deletion structural variations. Through this process, we initially screened out structural variants associated with the fruit peel color and size of Chinese cherry. In summary, this study provides valuable resources for population genetic relationships and will advance functional genomics studies in Chinese cherry and other crops.