A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'

Area of Science:

• Plant genomics
• Agricultural science
• Bioinformatics

Background:

• Genome sequencing advances Rosaceous crops, providing insights into traits like fruit quality and disease resistance.
• Understanding apple cultivar genomes is crucial for breeding and improving postharvest storage.

Purpose of the Study:

• To present the first haplotype-phased, chromosomal-level genome assembly for Malus domestica 'WA 38' (Cosmic Crisp®).
• To enable detailed genome-scale comparisons with other apple cultivars.
• To provide a reproducible and transparent genome assembly and annotation workflow.

Main Methods:

• Utilized short and long read sequencing data with a k-mer based approach for assembly.
• Assembled and segregated parental chromosomes into distinct haplomes (HapA from 'Honeycrisp', HapB from 'Enterprise').
• Employed BUSCO for assessing genome completeness and annotated gene content.

Main Results:

• Successfully generated two 650 Mb haplome assemblies (HapA and HapB) with 98.7% BUSCO completeness.
• Annotated 53,028 genes in HapA and 54,235 genes in HapB.
• Identified significant genome structure and gene family differences compared to 'Gala' and 'Honeycrisp' cultivars.

Conclusions:

• This is the first pome fruit genome fully phased into parental haplotypes, offering unprecedented detail.
• The genome assembly and annotation provide valuable resources for apple breeding and research.
• The shared, containerized workflow ensures transparency and reproducibility for future genome projects.