Haplotype-resolved chromosome-level genome assembly of Fragaria × ananassa Duch. cv. ‘Yuexin’

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Genome assembly and structural variation analysis of strawberry varieties are essential for understanding the genetic basis of fruit quality traits, such as fruit texture, organic acid content and aroma. In this study, we employed PacBio HiFi reads and Hi-C sequencing to generate a haplotype-resolved chromosome-level genome assembly of the improved strawberry cultivar ‘Yuexin’, which was selected from the crossing of ‘0362’ (‘Camarosa’ × ‘Akihime’) × ‘Sachinoka’. The assembly sizes of the primary assembly and two haplotypes were 875.84 Mb, 867.93 Mb and 823.17 Mb, with N50 length of 27.6 Mb, 27.3 Mb and 27.6 Mb respectively. Comprehensive genome comparison with its parent, cultivar ‘Camarosa’, identified numerous structural variants, which are positioned in the promoter or gene body regions. Some of these genes are involved in pathways related to cell wall, malate metabolism and fruit aroma. This dataset comprises the assembled genome sequence, annotations, and identified structural variants, providing new insights into the genetic basis of improved fruit quality.