Malus x domestica 'Fuji' Whole Genome v1.0.a2 Assembly & Annotation

Analysis NameMalus x domestica 'Fuji' Whole Genome v1.0.a2 Assembly & Annotation
MethodHifiasm (v0.15_r334)
SourcePacbio Fuji reads
Date performed2023-03-08


Li, W., Chu, C., Li, H. et al. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet (2024)


Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock ‘M9’, the semi-vigorous rootstock ‘MM106’ and ‘Fuji’, one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of ‘M9’, the major locus for rootstock-induced dwarfing. Comparing ‘M9’ and ‘MM106’ genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees.

Annotation of Whole Genome Assembly 

Unphased 49,972
Haplome A 49,597
Haplome B 49,117

Statistics of Genome Assembly

  Unphased Haplome A Haplome B
Genome size (bp) 736,974,467 692,808,547 671,417,791
GC content 38.46% 38.46% 38.36%
Genome sequence No. 1,360 208 164
Maximum genome sequence length (bp) 56,797,885 56,619,705 56,701,660
Minimum genome sequence length (bp) 11,736 13,308 13,501
Average genome sequence length (bp) 541,893 3,330,810 4,094,011
Genome sequence N50 (bp) 36,771,785 37,279,547 36,869,019
Genome sequence N90 (bp) 16,528,878 31,387,705 31,216,434

Homology of the Malus x domestica Fuji genome v1.0.a2 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

M. domestica v1.0.a2 proteins with arabidopsis (Araport11) homologs (EXCEL file) Mxdomestica_Fuji_v1.a2_vs_arabidopsis.xlsx.gz
M. domestica v1.0.a2 proteins with arabidopsis (Araport11) (FASTA file) Mxdomestica_Fuji_v1.a2_vs_arabidopsis_hit.fasta.gz
M. domestica v1.0.a2 proteins without arabidopsis (Araport11) (FASTA file) Mxdomestica_Fuji_v1.a2_vs_arabidopsis_noHit.fasta.gz
M. domestica v1.0.a2 proteins with SwissProt homologs (EXCEL file) Mxdomestica_Fuji_v1.a2_vs_swissprot.xlsx.gz
M. domestica v1.0.a2 proteins with SwissProt (FASTA file) Mxdomestica_Fuji_v1.a2_vs_swissprot_hit.fasta.gz
M. domestica v1.0.a2 proteins without SwissProt (FASTA file) Mxdomestica_Fuji_v1.a2_vs_swissprot_noHit.fasta.gz
M. domestica v1.0.a2 proteins with TrEMBL homologs (EXCEL file) Mxdomestica_Fuji_v1.a2_vs_trembl.xlsx.gz
M. domestica v1.0.a2 proteins with TrEMBL (FASTA file) Mxdomestica_Fuji_v1.a2_vs_trembl_hit.fasta.gz
M. domestica v1.0.a2 proteins without TrEMBL (FASTA file) Mxdomestica_Fuji_v1.a2_vs_trembl_noHit.fasta.gz

The Malus x domestica Fuji Genome v1.0.a2 assembly files are available in FASTA format.


Chromosomes (unphased) (FASTA file) Malus_x_domestica_Fuji_unphased_v1.0.a2.fasta.gz
Chromosomes (haplome A) (FASTA file) Malus_x_domestica_Fuji_HapA_v1.0.a2.fasta.gz
Chromosomes (haplome B) (FASTA file) Malus_x_domestica_Fuji_HapB_v1.0.a2.fasta.gz
Gene Predictions

The Malus x domestica Fuji v1.0.a2 genome gene prediction files are available in GFF3 and FASTA format.


Genes (unphased) (GFF3 file) Fuji_unphased.EVM_v1.0.a2.genes.gff3.gz
Genes (haplome A) (GFF3 file) Fuji_HapA_v1.0.a2.genes.gff3.gz
Genes (haplome B) (GFF3 file) Fuji_HapB_v1.0.a2.genes.gff3.gz
Protein sequences (unphased) (FASTA file) Fuji_unphased_v1.0.a2.pep.fasta.gz
Protein sequences (haplome A) (FASTA file) Fuji_HapA_v1.0.a2.pep.fasta.gz
Protein sequences (haplome B) (FASTA file) Fuji_HapB_v1.0.a2.pep.fasta.gz
CDS sequences (unphased) (FASTA file) Fuji_unphased_v1.0.a2.cds.fasta.gz
CDS sequences (haplome A) (FASTA file) Fuji_HapA_v1.0.a2.cds.fasta.gz
CDS sequences (haplome B) (FASTA file) Fuji_HapB_v1.0.a2.cds.fasta.gz
Functional Analysis

Functional annotation for the Malus x domestica Fuji genome v1.0.a2 are available for download below. The Malus x domestica Fuji Genome v1.0.a2 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 Mxdomestica_Fuji_v1.a2_genes2GO.xlsx.gz
IPR assignments from InterProScan Mxdomestica_Fuji_v1.a2_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Mxdomestica_Fuji_v1.a2_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Mxdomestica_Fuji_v1.a2_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 Fuji genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.


Malus x domestica GDR RefTrans v1 Mxdomestica_Fuji_v1.a2_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 Mxdomestica_Fuji_v1.a2_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Mxdomestica_Fuji_v1.a2_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Mxdomestica_Fuji_v1.a2_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Mxdomestica_Fuji_v1.a2_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Mxdomestica_Fuji_v1.a2_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Mxdomestica_Fuji_v1.a2_pyrus_GDR_reftransV1