High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'

Pfeifer, M.; Emeriewen, O. F.; Flachowsky, H.; Hoefer, M.; Keilwagen, J.; Lim, F.-S.; Peil, A.; Zetzsche, H.; Woehner, T. W.

doi:10.1101/2025.07.27.667097

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bioRxiv · 10.1101/2025.07.27.667097

High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'

Pfeifer, M.·Emeriewen, O. F.·Flachowsky, H.·Hoefer, M.·Keilwagen, J.·Lim, F.-S.·Peil, A.·Zetzsche, H.·Woehner, T. W.

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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.

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Pfeifer, M., Emeriewen, O. F., Flachowsky, H., Hoefer, M., Keilwagen, J., Lim, F.-S., Peil, A., Zetzsche, H., Woehner, T. W.. 2025-07-31. High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'. https://doi.org/10.1101/2025.07.27.667097

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