A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)-Reference-Cited by-同舟云学术

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

Published:2022-09-19 Issue: Volume:2022 Page:1-15
ISSN:2709-4715
Container-title:Gigabyte
language:
Short-container-title:Gigabyte

Author:

Khan Awais¹^ORCID,Carey Sarah B.²³^ORCID,Serrano Alicia¹^ORCID,Zhang Huiting⁴⁵^ORCID,Hargarten Heidi⁴^ORCID,Hale Haley²³^ORCID,Harkess Alex²³^ORCID,Honaas Loren⁴^ORCID

Affiliation:

1. Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA

2. Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA

3. HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA

4. USDA ARS Tree Fruit Research Lab, Wenatchee, WA 98801, USA

5. Department of Horticulture, Washington State University, Pullman, WA, USA

Abstract

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.

Funder

Washington Tree Fruit Research Commission

United States Department of Agriculture, Agricultural Research Service

New York State Department of Agriculture & Markets, Apple Research & Development Program

Publisher

GigaScience Press

Subject

General Agricultural and Biological Sciences

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