Malus x domestica cv. Gala Haploid Consensus Whole Genome v1.0 Assembly & Annotation

Analysis NameMalus x domestica cv. Gala Haploid Consensus Whole Genome v1.0 Assembly & Annotation
MethodDeNovoMAGIC3, Hifiasm and HiCanu64
SourceHaploid,Illumina and PacBio HiFi reads
Date performed2021-04-14


Sun X, Jiao C, Schwaninger H, Chao CT, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong GY, Fei Z. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication.. Nature genetics. 2020 Nov 02.


Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.



Homology of the Malus domestica cv. Gala Haploid Consensus 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 2018-05) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 


Protein Homologs

Malus_domestica Gala v1.0 proteins with NCBI nr homologs (EXCEL file) Malus_domestica_Gala_haploid_v1.0_vs_nr.xlsx.gz
Malus_domestica Gala v1.0 proteins with NCBI nr (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_nr_hit.fasta.gz
Malus_domestica Gala v1.0 proteins without NCBI nr (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_nr_noHit.fasta.gz
Malus_domestica Gala v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Malus_domestica_Gala_haploid_v1.0_vs_arabidopsis.xlsx.gz
Malus_domestica Gala v1.0 proteins with arabidopsis (Araport11) (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_arabidopsis_hit.fasta.gz
Malus_domestica Gala v1.0 proteins without arabidopsis (Araport11) (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_arabidopsis_noHit.fasta.gz
Malus_domestica Gala v1.0 proteins with SwissProt homologs (EXCEL file) Malus_domestica_Gala_haploid_v1.0_vs_swissprot.xlsx.gz
Malus_domestica Gala v1.0 proteins with SwissProt (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_swissprot_hit.fasta.gz
Malus_domestica Gala v1.0 proteins without SwissProt (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_swissprot_noHit.fasta.gz
Malus_domestica Gala v1.0 proteins with TrEMBL homologs (EXCEL file) Malus_domestica_Gala_haploid_v1.0_vs_trembl.xlsx.gz
Malus_domestica Gala v1.0 proteins with TrEMBL (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_trembl_hit.fasta.gz
Malus_domestica Gala v1.0 proteins without TrEMBL (FASTA file) Malus_domestica_Gala_haploid_v1.0_vs_trembl_noHit.fasta.gz



The Malus domestica cv. Gala Haploid Consensus Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Malus_domestica_Gala_haploid_v1.0.fasta.gz


Gene Predictions

The Malus domestica cv Gala v1.0 genome gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) Malus_domestica_Gala_haploid_v1.0.proteins.fasta.gz
CDS  (FASTA file) Malus_domestica_Gala_haploid_v1.0.cds.fasta.gz
Genes (GFF3 file) Malus_domestica_Gala_haploid_v1.0.genes.gff3.gz


Functional Analysis

Functional annotation for the Malus domestica cv. Gala Haploid Consensus Genome v1.0 are available for download below. The Malus_domestica Gala 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 Malus_domestica_Gala_haploid_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Malus_domestica_Gala_haploid_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Malus_domestica_Gala_haploid_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Malus_domestica_Gala_haploid_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 domestica cv. Gala haploid 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 Malus_domestica Gala_haploid_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Malus_domestica Gala_haploid_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Malus_domestica Gala_haploid_v1.0_pyrus_GDR_reftransV1