# High-quality haplotype-resolved genome assembly and annotation of Malus baccata ‘Jackii’

## TL;DR

This paper presents the first high-quality genome assembly of Malus baccata 'Jackii', a disease-resistant apple variety, which can aid in breeding new apple cultivars.

## Contribution

The study provides the first haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii' using advanced sequencing and bioinformatics methods.

## Key findings

- The genome assembly includes 17 pseudochromosomes with scaffold N50 values exceeding 30 Mb for both haplotypes.
- Over 42,000 genes were predicted and annotated with high accuracy, supported by BUSCO analysis exceeding 97.5%.
- The dataset is expected to support future genomic studies and improve apple breeding for disease resistance.

## Abstract

Malus baccata ‘Jackii’ has been observed to exhibit multiple disease resistances, thus rendering it a promising source for breeding new disease-resistant apple cultivars. Here, we present the first haplotype-resolved genome assembly and annotation of this genotype, achieved by integrating PacBio HiFi sequencing, Hi-C, and mRNA sequencing data with a range of bioinformatic tools and databases. The genome assembly comprises 17 pseudochromosomes with total scaffold lengths of 654.6 Mb and 637.5 Mb for the two haplotypes, respectively. Both haplotypes have scaffold N50 values exceeding 30 Mb, with 42,441 and 46,507 predicted genes, of which 99.9% were successfully annotated. The high quality of this genome is supported by BUSCO analysis values exceeding 97.5% for both haplotypes. This comprehensive dataset is well suited for a wide range of future genomic analyses and is anticipated to benefit apple breeding, particularly in the context of enhancing disease resistance.