Assembly and annotation of the ‘Golden Delicious’ Doubled-Haploid GDDH18 apple genome

Apple (Malus domestica Borkh.) is an important fruit crop cultivated worldwide in temperate regions. Due to their frequent high content in repetitive DNA sequences and large size, plant genomes have long been considered challenging to assemble. A first reference genome of a 'Golden Delicious' doubled-haploid apple tree, GDDH13, was previously produced in 2017. The chromosomes of GDDH13 present however a high percentage of N stretches, around 12%, and above 8% of the assembly was not anchored on chromosomes. Here, we provide a chromosome-level assembly of another 'Golden Delicious' doubled-haploid apple tree, GDDH18. Interestingly, this tree presents phenotypic differences with GDDH13, notably associated with fruits size. In this assembly, 99.4% of the sequences were assembled into 17 contigs corresponding to the 17 expected chromosomes of apple, and all but one of these 17 contigs present telomeric repeats at both their extremities. A high complete BUSCO (Benchmarking Universal Single-Copy Orthologs) score and a high LTR Assembly Index, respectively of 99.5% and above 22, attest to the high quality of the assembly and to the completeness of both the gene and the repetitive space. A de novo annotation of the assembly was produced, allowing to predict 51,892 protein-coding genes, of which 93% are functionally annotated. A total of 6,239 additional genes were functionally annotated in comparison with the GDDH13 assembly. This high-quality assembly of GDDH18 along with a de novo annotation will both help to better understand the phenotypic differences between the trees GDDH13 and GDDH18, and will serve as an enhanced reference genome for advancing the study of apple genomics.