The chromosome-level haploid genome Assembly of Malus domestica ‘Fuji’

Apple (Malus domestica) is one of the main cultivated fruit trees in China, and the 'Red Fuji' apple (Malus domestica cv. Red Fuji) is the predominant apple cultivar in the country. Molecular-assisted breeding based on genomic sequence information has made significant achievements in apple breeding. Genome sequencing and annotation provide a more comprehensive understanding of genetic information, especially species-specific genes. Analysing the haploid genome of a heterozygous diploid organism helps explore the differential gene expression derived from the parental genomes. We have successfully deciphered the haploid genome of the 'Red Fuji' apple, and the complete and accurate haploid genome provides a solid foundation for subsequent comparative genomics and transcriptome analyses. In the future, further integration of the Fuji apple genome with other omics data will enhance our understanding of the biological characteristics of the Fuji apple. This will facilitate apple quality improvement and the development of new apple varieties through targeted breeding efforts. By harnessing the power of genomics and molecular-assisted breeding, we can identify desirable traits and accelerate the breeding process, ultimately leading to the production of improved apple cultivars that meet the demands of consumers and the industry.