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

View ORCID ProfileAwais Khan, View ORCID ProfileSarah B. Carey, View ORCID ProfileAlicia Serrano, View ORCID ProfileHuiting Zhang, View ORCID ProfileHeidi Hargarten, View ORCID ProfileHaley Hale, View ORCID ProfileAlex Harkess, View ORCID ProfileLoren Honaas
doi: https://doi.org/10.1101/2022.08.24.505160
Awais Khan
1Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
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  • For correspondence: awais.khan@cornell.edu loren.honaas@usda.gov
Sarah B. Carey
2Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
3HudsonAlpha Institute for Biotechnology, Huntsville AL, 35806, USA
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Alicia Serrano
1Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
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Huiting Zhang
4USDA ARS Tree Fruit Research Lab, Wenatchee, WA 98801, USA
5Department of Horticulture, Washington State University, Pullman, WA USA
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Heidi Hargarten
4USDA ARS Tree Fruit Research Lab, Wenatchee, WA 98801, USA
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Haley Hale
2Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
3HudsonAlpha Institute for Biotechnology, Huntsville AL, 35806, USA
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Alex Harkess
2Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
3HudsonAlpha Institute for Biotechnology, Huntsville AL, 35806, USA
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Loren Honaas
4USDA ARS Tree Fruit Research Lab, Wenatchee, WA 98801, USA
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  • ORCID record for Loren Honaas
  • For correspondence: awais.khan@cornell.edu loren.honaas@usda.gov
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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 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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 25, 2022.
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A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)
Awais Khan, Sarah B. Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas
bioRxiv 2022.08.24.505160; doi: https://doi.org/10.1101/2022.08.24.505160
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A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)
Awais Khan, Sarah B. Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas
bioRxiv 2022.08.24.505160; doi: https://doi.org/10.1101/2022.08.24.505160

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