A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

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The apple cultivar ‘Honeycrisp’ has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of ‘Honeycrisp’ apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8–97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most ‘Honeycrisp’ genes are assigned into orthogroups shared with other genomes, with 121 ‘Honeycrisp’-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts.

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  1. Abstract

    This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.69), and has published the reviews under the same license. These are as follows.

    Reviewer 1. Dr.Liyi Zhang

    ‘Honeycrisp’ is known for its exceptionally crisp and juicy texture as a source of interesting genetic diversity in apple breeding programs worldwide. In addition, high quality genomes are required for us to understanding the genetic characteristics of a core cultivar, This study presents a fully phased, chromosome-level high-quality apple genome with a higher contiguity and completeness than previously sequenced apple genomes and also reveals 121 ‘Honeycrisp’-specific orthogroups with a large data set, which provide a toolbox for apple genetic research and breeding.

    The paper is well written and the data is convincing. So, I recommend to publish this paper ASAP.

    **Reviewer 2. Luca Bianco **

    Are all data available and do they match the descriptions in the paper?

    I could not access to the Bioproject data nor see the results files (i.e. fasta, gff,...) but I am confident they will be available once the paper is accepted.

    Is there sufficient data validation and statistical analyses of data quality?

    The only exception is what I mentioned regarding the haplotype separation (see general comments below).

    General comments: This paper describes the genome sequence of Honeycrisp, an important apple cultivar, produced with the latest sequencing technologies and assembled into phased chromosomes. In my opinion, the manuscript is well written, very interesting and certainly worth publication. There are only a few points that I would like to see addressed:

    1. How can you be sure that the two haplomes are a good representation of each chromosome and not a mix of the two haplotypes? In other words, have you checked that the whole sequence of each chromosome represents one phase only? It would be great if you could provide some data (e.g. SNPs,...) to support this and discuss the results obtained in this regard.

    2. Some additional stats regarding the obtained sequence could be added to table 2 and/or table 5 (e.g. number of Ns in the genome, how many telomers were assembled in each chromosome -- if not all telomers were identified, )

    3. The gene family analysis among the different apple genomes is quite interesting but rather superficial. It would be nice to dig deeper into the function of the orthogroups that are unique to Honeycrisp, describe what pathways they are involved in and so on...