Malus x domestica ‘Honeycrisp’ Genome v1.1.a1 Assembly & Annotation

Analysis NameMalus x domestica ‘Honeycrisp’ Genome v1.1.a1 Assembly & Annotation
MethodHifiasm (v0.16.1)
SourcePacBio reads Malus x domestica ‘Honeycrisp’ Genome v1.1.a1
Date performed2022-09-15


Awais Khan, Sarah B. Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas, A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica),Gigabyte,2022 (GDR | Journal)


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.

Summary of ‘Honeycrisp’ genome assembly statistics

Assembly Length


of Contigs

Longest contig (bp)

N50 L50

Protein-coding genes


completeness (%)

Haplome A 674,476,353 473 55,653,390 32,818,62 9 47,563 82.7 98.6
Haplome B 660,238,068 215 56,154,892 31,578,807 9 48,655 83 98.7

Homology of the Malus x domestica Honeycrisp Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

Malus x domestica v1.0 proteins with NCBI nr homologs (EXCEL file) mxd_Honeycrisp_v1.0_vs_nr.xlsx.gz
Malus x domestica v1.0 proteins with NCBI nr (FASTA file) mxd_Honeycrisp_v1.0_vs_nr_hit.fasta.gz
Malus x domestica v1.0 proteins without NCBI nr (FASTA file) mxd_Honeycrisp_v1.0_vs_nr_noHit.fasta.gz
Malus x domestica v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) mxd_Honeycrisp_v1.0_vs_arabidopsis.xlsx.gz
Malus x domestica v1.0 proteins with arabidopsis (Araport11) (FASTA file) mxd_Honeycrisp_v1.0_vs_arabidopsis_hit.fasta.gz
Malus x domestica v1.0 proteins without arabidopsis (Araport11) (FASTA file) mxd_Honeycrisp_v1.0_vs_arabidopsis_noHit.fasta.gz
Malus x domestica v1.0 proteins with SwissProt homologs (EXCEL file) mxd_Honeycrisp_v1.0_vs_swissprot.xlsx.gz
Malus x domestica v1.0 proteins with SwissProt (FASTA file) mxd_Honeycrisp_v1.0_vs_swissprot_hit.fasta.gz
Malus x domestica v1.0 proteins without SwissProt (FASTA file) mxd_Honeycrisp_v1.0_vs_swissprot_noHit.fasta.gz
Malus x domestica v1.0 proteins with TrEMBL homologs (EXCEL file) mxd_Honeycrisp_v1.0_vs_trembl.xlsx.gz
Malus x domestica v1.0 proteins with TrEMBL (FASTA file) mxd_Honeycrisp_v1.0_vs_trembl_hit.fasta.gz
Malus x domestica v1.0 proteins without TrEMBL (FASTA file) mxd_Honeycrisp_v1.0_vs_trembl_noHit.fasta.gz



The Malus x domestica Honeycrisp Genome v1.1 assembly files are available in FASTA format.


Chromosomes (haplome A) (FASTA file) Malus_x_domestica_Honeycrisp_HAP1_v1.1.a1.fasta.gz
Chromosomes (haplome B) (FASTA file) Malus_x_domestica_Honeycrisp_HAP2_v1.1.a1.fasta.gz


Gene Predictions

The Malus x domestica Honeycrisp v1.1 genome gene prediction files are available in GFF3 and FASTA format.


Genes (haplome A) (GFF3 file) Honeycrisp_HAP1_v1.1.a1.genes.gff3.gz
Genes (haplome B) (GFF3 file) Honeycrisp_HAP2_v1.1.a1.genes.gff3.gz
Protein sequences (haplome A) (FASTA file) Honeycrisp_HAP1_v1.1.a1.pep.fasta.gz
Protein sequences (haplome B) (FASTA file) Honeycrisp_HAP2_v1.1.a1.pep.fasta.gz
CDS sequences (haplome A) (FASTA file) Honeycrisp_HAP1_v1.1.a1.cds.fasta.gz
CDS sequences (haplome B) (FASTA file) Honeycrisp_HAP2_v1.1.a1.cds.fasta.gz


Functional Analysis

Functional annotation for the Malus x domestica Honeycrisp Genome v1.0 are available for download below. The Malus x domestica Honeycrisp Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).


GO assignments from InterProScan mxd_Honeycrisp_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan mxd_Honeycrisp_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs mxd_Honeycrisp_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways mxd_Honeycrisp_v1.0_KEGG-pathways.xlsx.gz


Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Malus x domestica Honeycrisp genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.


Fragaria x ananassa GDR RefTrans v1 mxd_Honeycrisp_v1.0_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 mxd_Honeycrisp_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 mxd_Honeycrisp_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 mxd_Honeycrisp_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 mxd_Honeycrisp_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 mxd_Honeycrisp_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 mxd_Honeycrisp_v1.0_pyrus_GDR_reftransV1