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

Authors: KHAN, AWAIS - Cornell University; CAREY, SARAH - Auburn University; SERRANO, ALICIA - Cornell University; ZHANG, HUITING - Washington State University; Hargarten, Heidi; HALE, HALEY - Auburn University; HARKESS, ALEX - Auburn University; Honaas, Loren

Submitted to: GigaByte
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2022
Publication Date: 9/19/2022
Citation: Khan, A., Carey, S., Serrano, A., Zhang, H., Hargarten, H.L., Hale, H., Harkess, A., Honaas, L.A. 2022. A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica). GigaByte. https://doi.org/10.1101/2022.08.24.505160.
DOI: https://doi.org/10.1101/2022.08.24.505160

Interpretive Summary: ‘Honeycrisp’ is one of the most valuable apple cultivars grown in the United States. The crisp juicy texture and superior taste attracted millions of consumers to pay twice as much money for this amazing eating experience. It is also a popular breeding parent and nine new cultivars derived from ‘Honeycrisp’ are on the market. However, little is know about which genes are linked to these desirable traits and how some traits are inherited by the new cultivars while some are not. To gain a deeper understanding of the aforementioned questions, researchers need to investigate the ‘Honeycrisp’ apple’s genetic composition down to each building block, namely studying the genome at a nucleotide-level. Three apple cultivars have their genomes sequenced so far, namely ‘Gala’, ‘Hanfu’, and ‘Golden Delicious’, giving valuable insights into what makes an apple in general, but more cultivar genomes are needed to understand the difference between cultivars. The most efficient way to learn more about cultivar-specific traits is through understanding the genetic basis of these traits which can be achieved by comparing, base-by-base, those cultivar genomes. One analogy that is relevant to everybody’s daily life in the last a few years would be the Coronavirus. Deciphering and comparing genomes of different Coronavirus strains allowed researchers to understand mutations that affected virulence and transmissibility of the virus and further provided suggestions on vaccination, and management strategies for both the current and potentially new strains.

Technical Abstract: ‘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 resistance to disease. However, it suffers from a number of physiological disorders and is susceptible to production and post-harvest 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 the ‘Honeycrisp’ apple, using PacBio HiFi, Omni-C, and Illumina sequencing approaches. 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. Our assembly is by far the most contiguous among all the apple genomes. 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 apples, but it also reveals 121 ‘Honeycrisp’-specific orthogroups. Our data present a valuable resource for understanding genetic basis associated with agronomically important traits such as fruit quality, abiotic stress tolerance, and disease resistance in apples, and can facilitate molecular breeding programs.