Malus baccata haplotype resolved genome assembly

The assemblies of both haplotypes MbMAL0419_HT1_1.0 and MbMAL0419_HT2_1.0 are based on 144x PACBio CCS data, 135x of 150bp paired-end Illumina Novaseq 6000, and 330x Hi-C data. The assembly was performed due to the following steps: primary assemblies generation after removal of low-quality reads and sequence adapters from CCS data with an N50 value of 16,81 kb using Hifiasm (v 0.16). Chromosome-scale scaffolding for both haplotypes was performed with 206 Gb clean data generated from the Hi-C library and mapped to the preliminary assemblies using BWA BWA (Ver. 0.7.10-r789) with the default parameters. For each haplotype 17 chromosome-scale scaffolds were assigned by synteny based on Malus domestica.