Malus x domestica Golden Delicious FEM v1.1

Overview
Analysis NameMalus x domestica Golden Delicious FEM v1.1
MethodHifiasm (v.0.19.0)
SourcePacBio HiFi reads
Date performed2025-03-20

Publication

To be submitted (data submitted by Luca Bianco, FEM Research and Innovation Center, Italy)

Methods

PacBio HiFi reads (41Gb, ~55x coverage) have been assembled together with Omni-C reads using hifiasm assembler v.0.19.0 (Cheng, et al., Nature Methods, 2021). The resulting contigs were scaffolded into chromosomes using a dense integrated genetic map (Di Pierro et al., Hortic. Research, 2016). Phasing was checked with a set of ~10K Golden Delicious phased SNPs coming from the Infinium Apple 20K array (Bianco et. al., PLoSOne, 2016).

Assembly

The Malus x domestica Golden Delicious FEM Genome v1.1 assembly files are available in FASTA format.

Downloads

Chromosomes (haplome A) (FASTA file) Golden_Delicious_FEM_HAP1_v1.1.fasta.gz
Chromosomes (haplome B) (FASTA file) Golden_Delicious_FEM_HAP2_v1.1.fasta.gz
Gene Predictions

The Malus x domestica Golden Delicious FEM Genome v1.1 gene prediction file are available in GFF3 and FASTA format.

Downloads

Genes (haplome A) (GFF3 file) Golden_Delicious_FEM_HAP1_v1.1.genes.gff3.gz
Genes (haplome B) (GFF3 file) Golden_Delicious_FEM_HAP2_v1.1.genes.gff3.gz
Protein sequences (haplome A) (FASTA file) Golden_Delicious_FEM_HAP1_v1.1.protein.fasta.gz
Protein sequences (haplome B) (FASTA file) Golden_Delicious_FEM_HAP2_v1.1.protein.fasta.gz
CDS (haplome A) (FASTA file) Golden_Delicious_FEM_HAP1_v1.1.cds.fasta.gz
CDS (haplome B) (FASTA file) Golden_Delicious_FEM_HAP2_v1.1.cds.fasta.gz