PT  - JOURNAL ARTICLE
AU  - Awais Khan
AU  - Sarah B. Carey
AU  - Alicia Serrano
AU  - Huiting Zhang
AU  - Heidi Hargarten
AU  - Haley Hale
AU  - Alex Harkess
AU  - Loren Honaas
TI  - A phased, chromosome-scale genome of ‘Honeycrisp’ apple (<em>Malus domestica</em>)
AID  - 10.1101/2022.08.24.505160
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.08.24.505160
4099  - http://biorxiv.org/content/early/2022/08/25/2022.08.24.505160.short
4100  - http://biorxiv.org/content/early/2022/08/25/2022.08.24.505160.full
AB  - ‘Honeycrisp’ is one of the most valuable apple cultivars grown in the United States and a popular breeding parent due to its superior fruit quality traits, high levels of cold hardiness, and disease resistance. However, it suffers from a number of physiological disorders and is susceptible to production and postharvest issues. Although several apple genomes have been sequenced in the last decade, there is still a substantial knowledge gap in understanding the genetic mechanisms underlying cultivar-specific traits. Here we present a fully phased, chromosome-level genome of ‘Honeycrisp’ apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms. Our genome assembly is by far the most contiguous among all the apple genomes. The sizes of the two assembled haplomes are 674 Mb and 660 Mb, with contig N50s of 32.8 Mb and 31.6 Mb, respectively. In total, 47,563 and 48,655 protein coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database, the most complete among all Malus annotations. A gene family analysis using seven Malus genomes shows that a vast majority of ‘Honeycrisp’ genes are assigned into orthogroups shared with other genomes, but it also reveals 121 ‘Honeycrisp’-specific orthogroups. We provide a valuable resource for understanding the genetic basis of horticulturally important traits in apples and other related tree fruit species, including at-harvest and postharvest fruit quality, abiotic stress tolerance, and disease resistance, all of which can enhance breeding efforts in Rosaceae.Competing Interest StatementThe authors have declared no competing interest.