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The assembly drMalSylv7.2 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation ... with Hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Malus domestica (apple) GCA_004115385.1. Shared sequences between chromosomes are visible in the Hi-C map in agreement with the findings of
https://doi.org/10.1038/ng.654 for Malus domestica. The Hi-C map provides evidence of inversions between haplotypes in chromosome 2 - 24.82-26.19Mb, and chromosome 11 - 17.06-19.05Mb. There are several scaffolds that it was possible to localize to a chromosome but not place, these have been labelled as unloc. Two of the largest unlocalised scaffolds -SUPER_4_unloc_1 and SUPER_14_unloc_1 - appear to be larger haplotypes of two specific loci; Chromosome 4 at 
26.13-26.31Mb and Chromosome 14 at 
782kb respectively. From the Hi-C it appears that these loci currently represent the shorter haplotype. As there is some uncertainty over these unloc scaffolds they have been left in the primary assembly.  more

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