Malus ioensis Genome v1.0 Assembly & Annotation

Overview
Analysis NameMalus ioensis Genome v1.0 Assembly & Annotation
MethodHifiasm (v0.16.1)
SourceHi-C reads
Date performed2024-09-18

Publication

Švara, A., Sun, H., Fei, Z., et al. 2024, Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples. DNA Res., dsae026, 2024.05.13.593769. https://doi.org/10.1093/dnares/dsae026

 

Homology

Homology of the Malus ioensis 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

M. ioensis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Malus_ioensis_v1.0_vs_arabidopsis.xlsx.gz
M. ioensis v1.0 proteins with arabidopsis (Araport11) (FASTA file) Malus_ioensis_v1.0_vs_arabidopsis_hit.fasta.gz
M. ioensis v1.0 proteins without arabidopsis (Araport11) (FASTA file) Malus_ioensis_v1.0_vs_arabidopsis_noHit.fasta.gz
M. ioensis v1.0 proteins with SwissProt homologs (EXCEL file) Malus_ioensis_v1.0_vs_swissprot.xlsx.gz
M. ioensis v1.0 proteins with SwissProt (FASTA file) Malus_ioensis_v1.0_vs_swissprot_hit.fasta.gz
M. ioensis v1.0 proteins without SwissProt (FASTA file) Malus_ioensis_v1.0_vs_swissprot_noHit.fasta.gz
M. ioensis v1.0 proteins with TrEMBL homologs (EXCEL file) Malus_ioensis_v1.0_vs_trembl.xlsx.gz
M. ioensis v1.0 proteins with TrEMBL (FASTA file) Malus_ioensis_v1.0_vs_trembl_hit.fasta.gz
M. ioensis v1.0 proteins without TrEMBL (FASTA file) Malus_ioensis_v1.0_vs_trembl_noHit.fasta.gz
Assembly

The Malus ioensis Genome v1.0 assembly files are available in FASTA format.

Downloads

Chromosomes (Haplome A) (FASTA file) Malus_ioensis_hap1_v1.0.a1.fa.gz
Chromosomes (Haplome B) (FASTA file) Malus_ioensis_hap2_v1.0.a1.fa.gz
Gene Predictions

The Malus ioensis v1.0.a1 genome gene prediction file are available in GFF3 and FASTA format.

Downloads

Genes (Haplome A) (GFF3 file) Malus_ioensis_hap1_v1.0.a1.genes.gff3.gz
Genes (Haplome B) (GFF3 file) Malus_ioensis_hap2_v1.0.a1.genes.gff3.gz
Protein sequences (Haplome A) (FASTA file) Malus_ioensis_hap1_v1.0.a1.protein.fa.gz
Protein sequences (Haplome B) (FASTA file) Malus_ioensis_hap2_v1.0.a1.protein.fa.gz
CDs (Haplome A) (FASTA file) Malus_ioensis_hap1_v1.0.a1.cds.fa.gz
CDs (Haplome B) (FASTA file) Malus_ioensis_hap2_v1.0.a1.cds.fa.gz
Functional Analysis

Functional annotation for the Malus ioensis genome v1.0 are available for download below. The Malus ioensis 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).

Downloads

GO assignments from InterProScan Malus_ioensis_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Malus_ioensis_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Malus_ioensis_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Malus_ioensis_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 ioensis 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_ioensis_v1.0_f.x.ananassa_GDR_reftransV1
P. armeniaca GDR RefTrans v1 Malus_ioensis_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Malus_ioensis_v1.0_p.persica_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Malus_ioensis_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Malus_ioensis_v1.0_pyrus_GDR_reftransV1