Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation

Analysis NameMalus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
MethodBfast, in house developed software
Sourcea de novo assembly of a 'Golden Delicious' doubled-haploid tree (GDDH13)
Date performed2017-08-07


Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E. (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature genetics. 49, 1099–1106


To produce a high-quality apple reference genome and methylome, a de novo assembly of a 'Golden Delicious' doubled-haploid tree (GDDH13) composed of 280 assembled scaffolds and arranged into 17 pseudomolecules, which represent the 17 chromosomes of apple, has been generated. This assembly resulted from a combination of short (Illumina) and long sequencing reads (PacBio), along with scaffolding based on optical maps (BioNano) and a high-density integrated genetic linkage map23. This chromosome-scale assembly was complemented by a detailed de novo annotation of genes based on RNA sequencing (RNA-seq) data, TE annotation and small RNA alignments.


Homology of the Malus x domestica GDDH13v1.1 transcript swas determined by pairwise sequence comparison using the blastx algorithm against various protein databases. The results are available for download in Excel format. An expectation value cutoff less than 1e-6 was used for Arabidoposis proteins (TAIR10) and 1e-9  for the NCBI nr, Uniprot SwissProt, and Uniprot TrEMBL databases.


Protein Homologs

Malus x domestica transcripts with NCBI nr homologs Malus_x_domestica_GDDH13_v1.1_vs_nr.xlsx
Malus x domestica transcripts with NCBI arabidopsis (TAIR10) homologs Malus_x_domestica_GDDH13_v1.1_vs_tair.xlsx
Malus x domestica transcripts with NCBI swissprot homologs Malus_x_domestica_GDDH13_v1.1_vs_swissprot.xlsx
Malus x domestica transcripts with NCBI trembl homologs Malus_x_domestica_GDDH13_v1.1_vs_trembl.xlsx



All assembly and annotation files are available for download by selecting the desired data type in the left-hand side bar.  Each data type page will provide a description of the available files and links to download.



Pseudomolecule (FASTA file) GDDH13_1-1_formatted.fasta.gz


Gene Predictions


mRNA sequences (FASTA file) GDDH13_1-1_mrna.fasta.gz
Protein sequences  (FASTA file) GDDH13_1-1_prot.fasta.gz
Gene models (GFF3 file) gene_models_20170612.gff3.gz


Functional Analysis

Functional annotations for the Malus x domestica GDDH13 v1.1 genome are available for download below. The Malus x domestica transcripts 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).


InterPro Domains Malus_x_domestica_GDDH13_v1.1_interpro.txt.tar.gz
Transcripts mapped to KEGG Orthologs (March 2024) Malus_x_domestica_GDDH13_v1.1_KEGG-orthologis.txt.gz
Transcripts mapped to KEGG Pathways (March 2024) Malus_x_domestica_GDDH13_v1.1_KEGG-pathways.txt.gz

Alignments of SNP arrays to GDDH13 v1.1

SNP array provided by File
480K SNP array for Malus x domestica (Bianco et al. 2016) Nicolas Daccord (Daccord et al. 2017) 480K_snp_pos_GDDH13.gff3
IRSC 9K SNP array for apple (Chagné et et al. 2012 Stijn Vanderzande (Vanderzande et al. 2020) 9K_SNP_positions_DH_genome.xlsx