Malus x domestica WA 38 Genome v1.0 Assembly & Annotation

Overview
Analysis NameMalus x domestica WA 38 Genome v1.0 Assembly & Annotation
MethodHifiasm (v0.16.1)
SourceOmni-C data; PacBio HiFi long reads
Date performed2024-04-11

Publication: Zhang, H., Ko, I., Eaker, A., Haney, S., Khuu, N., Ryan, K., Appleby, A. B., Hoffmann, B., Landis, H., Pierro, K. A., Willsea, N., Hargarten, H., Yocca, A. E., Harkess, A., Honaas, L., & Ficklin, S. (2024). A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. ‘WA 38’. G3: Genes|Genomes|Genetics. https://doi.org/10.1093/g3journal/jkae222

 

Statistics of Genome Assembly

  Haplome A Haplome B
Number of Scaffold 17 17
Haploid genome size (Mb) 645.41 651.07
N50 (Mb)  36.1 37.2 
L50 8 8
Number of proteincoding genes  53,028 54,235
Complete BUSCO (%) Assembly 98.7 98.7
Complete BUSCO (%) Annotation  98.5 98.4
Number of orthogroups in 26Gv2.0  10,494 10,511
Homology

Homology of the Malus x domestica WA 38 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-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

Malus x domestica WA 38 v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) WA_38_v1.0_vs_arabidopsis.xlsx.gz
Malus x domestica WA 38 v1.0 proteins with arabidopsis (Araport11) (FASTA file) WA_38_v1.0_vs_arabidopsis_hit.fasta.gz
Malus x domestica WA 38 v1.0 proteins without arabidopsis (Araport11) (FASTA file) WA_38_v1.0_vs_arabidopsis_noHit.fasta.gz
Malus x domestica WA 38 v1.0 proteins with SwissProt homologs (EXCEL file) WA_38_v1.0_vs_swissprot.xlsx.gz
Malus x domestica WA 38 v1.0 proteins with SwissProt (FASTA file) WA_38_v1.0_vs_swissprot_hit.fasta.gz
Malus x domestica WA 38 v1.0 proteins without SwissProt (FASTA file) WA_38_v1.0_vs_swissprot_noHit.fasta.gz
Malus x domestica WA 38 v1.0 proteins with TrEMBL homologs (EXCEL file) WA_38_v1.0_vs_trembl.xlsx.gz
Malus x domestica WA 38 v1.0 proteins with TrEMBL (FASTA file) WA_38_v1.0_vs_trembl_hit.fasta.gz
Malus x domestica WA 38 v1.0 proteins without TrEMBL (FASTA file) WA_38_v1.0_vs_trembl_noHit.fasta.gz
Assembly

The Malus x domestica WA 38 Genome v1.0 assembly files are available in FASTA format.

Downloads

Chromosomes (haplome A) (FASTA file) Malus_x_domestica_WA_38_HAP1_v1.0.a1.fasta.gz
Chromosomes (haplome B) (FASTA file) Malus_x_domestica_WA_38_HAP2_v1.0.a1.fasta.gz
Chromosomes (haplome A) (softmasked FASTA file) Malus_x_domestica_WA_38_HAP1_v1.0.a1.softmasked.fasta.gz
Chromosomes (haplome B) (softmasked FASTA file) Malus_x_domestica_WA_38_HAP2_v1.0.a1.softmasked.fasta.gz
Chromosomes (haplome A) (Xmasked FASTA file) Malus_x_domestica_WA_38_HAP1_v1.0.a1.Xmasked.fasta.gz
Chromosomes (haplome B) (Xmasked FASTA file) Malus_x_domestica_WA_38_HAP2_v1.0.a1.Xmasked.fasta.gz
Chromosomes (haplome A) (Repeat FASTA file) Malus_x_domestica_WA_38_HAP1_v1.0.a1.repeat.fasta.gz
Chromosomes (haplome B) (Repeat FASTA file) Malus_x_domestica_WA_38_HAP2_v1.0.a1.repeat.fasta.gz
Chromosomes (haplome A) (TE FASTA file) Malus_x_domestica_WA_38_HAP1_v1.0.a1.EDTA.TElib.fasta.gz
Chromosomes (haplome B) (TE FASTA file) Malus_x_domestica_WA_38_HAP2_v1.0.a1.EDTA.TElib.fasta.gz
Gene Predictions

The Malus x domestica WA 38 v1.0.a1 genome gene prediction file are available in GFF3 and FASTA format.

Downloads

Genes (haplome A) (GFF3 file) WA_38_HAP1_v1.0.a1.genes.gff3.gz
Genes (haplome A) (GFF3 file) WA_38_HAP2_v1.0.a1.genes.gff3.gz
Gene sequences (haplome A) (FASTA file) WA_38_HAP1_v1.0.a1.gene.fna.gz
Gene sequences (haplome B) (FASTA file) WA_38_HAP2_v1.0.a1.gene.fna.gz
Protein sequences (haplome A) (FASTA file) WA_38_HAP1_v1.0.a1.protein.faa.gz
Protein sequences (haplome B) (FASTA file) WA_38_HAP2_v1.0.a1.protein.faa.gz
mRNA sequences (haplome A) (FASTA file) WA_38_HAP1_v1.0.a1.mRNA.fna.gz
mRNA sequences (haplome B) (FASTA file) WA_38_HAP2_v1.0.a1.mRNA.fna.gz
CDS sequences (haplome A) (FASTA file) WA_38_HAP1_v1.0.a1.cds.fna.gz
CDS sequences (haplome B) (FASTA file) WA_38_HAP2_v1.0.a1.cds.fna.gz
Functional Analysis

Functional annotation for the Malus x domestica WA 38 genome v1.0 are available for download below. The Malus x domestica WA 38 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 Mxdomestica-WA_38_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Mxdomestica-WA_38_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Mxdomestica-WA_38_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Mxdomestica-WA_38_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 WA 38 genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.

 

Fragaria x ananassa GDR RefTrans v1 Malus_x_domestica-WA_38_v1.0_f.x.ananassa_GDR_reftransV1
P. armeniaca GDR RefTrans v1 Malus_x_domestica-WA_38_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Malus_x_domestica-WA_38_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Malus_x_domestica-WA_38_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Malus_x_domestica-WA_38_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Malus_x_domestica-WA_38_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Malus_x_domestica-WA_38_v1.0_pyrus_GDR_reftransV1