Accurate genome assemblies and structural gene annotation are critical for genomic studies. Using second- (Illumina) and third-generation sequencing (PacBio) and optical mapping technologies (BioNano), we have generated a high quality genome assembly of the apple tree. Our de novo assembly resulted in a genome of 649.7 Mb, with a N50 of 5.6 Mb. Seventeen pseudo-chromosomes were constructed, representing 96.3% of the sequence data. We propose an evaluation of genome assembly tools using a medium long reads coverage. Using mRNA, EST and RNA-seq libraries, a first gene prediction modelling identified 42,140 protein coding genes. An evaluation of the impact of different RNA-seq data pre-processing methods on the annotation was performed using BUSCO and a set of 865 manually expertised genes as a reference.
