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

Abstract 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 scaffold sequences. We further obtained resequencing data of 8 Chinese cherry varieties at an average sequencing depth of about 104× per individual. Population structure analysis revealed that the 8 varieties were partitioned into two distinct groups, and the G matrix analysis found that the closest genetic background was shared between the ‘Changbing’ and ‘Duanbing’ varieties. In addition, we have creatively established a workflow for transforming heterozygous genotypes from diploid format to tetraploid format by conducting secondary genotyping in deletion structural variations, and through this process, structural variants related to Chinese cherry fruit peel color or size were initially screened out. In summary, this study provides valuable resources for population genetic relationships and will promote functional genomics studies in Chinese cherry and other crops.