ArticleGigaByte (Hong Kong, China)2022
A phased, chromosome-scale genome of 'Honeycrisp' apple (
Article in GigaByte (Hong Kong, China), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm.PLoS genetics · 2026Article
- Article
- An X-linked sex determination mechanism in cannabis and hop.Nature communications · 2026Article
- Haplotype-phased 'Ottawa 3' genome unravels differential reaction of apple rootstock roots to mixed viral infection.The Plant journal : for cell and molecular biology · 2026Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
- Genome Assembly Revealed MdZAT5 Coordinates Anthocyanin Biosynthesis in Apple Fruit Peel and Flesh by Interacting With MdHY5.Plant biotechnology journal · 2026Article
- Haplotype-resolved chromosome-level genome assemblies of nineteen apple (Malus domestica Borkh.) cultivars.Scientific data · 2026Article
- Convergent domestication of bitter apples and pears by selecting mutations of MYB transcription factors to reduce proanthocyanidin levels.Molecular horticulture · 2025Article
- An X-linked sex determination mechanism in cannabis and hop.bioRxiv : the preprint server for biology · 2025Article
- Pan-genome analysis reveals the evolution and diversity of Malus.Nature genetics · 2025Article
- Guidelines for gene and genome assembly nomenclature.Genetics · 2025Article
- Genome sequencing of 'Fuji' apple clonal varieties reveals genetic mechanism of the spur-type morphology.Nature communications · 2024Article
- Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Pomological and Molecular Characterization of Apple Cultivars in the German Fruit Genebank.Plants (Basel, Switzerland) · 2024Article
- Widespread application of apomixis in agriculture requires further study of natural apomicts.iScience · 2024Review
- A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'.G3 (Bethesda, Md.) · 2024Article
- Genomic data provides insights into the evolutionary history and adaptive differentiation of two tetraploid strawberries.Horticulture research · 2024Article
- Article
- A chromosome-scale assembly for 'd'Anjou' pear.G3 (Bethesda, Md.) · 2024Article
- Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing.Nature genetics · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.