Malus x domestica Golden Delicious Genome NCBI annotation

Overview
Analysis NameMalus x domestica Golden Delicious Genome NCBI annotation
MethodDBG2OLC; SOAPdenovo2 ; BESST (v. May-2016)
SourceIllumina; PacBio; BioNano
Date performed2023-10-30

Publication: 

Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E. (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature genetics. 49, 1099–1106

Original Annotation Data is available at Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation

Assembly statistics (Re-annotation done by NCBI)

  RefSeq GenBank
Genome size 703 Mb 703 Mb
Total ungapped length 625.3 Mb 625.3 Mb
Number of chromosomes 17 17
Number of organelles 1 0
Number of scaffolds 806 806
Scaffold N50 37.6 Mb 37.6 Mb
Scaffold L50 9 9
Number of contigs 7,496 7,496
Contig N50 588.9 kb 588.9 kb
Contig L50 329 329
GC percent 38 38
Genome coverage 700.0x 700.0x
Assembly level Chromosome Chromosome
BUSCO analysis (4.0.2)
Single-copy  60.7%
Duplicated  37.1%  
Fragmented  0.5%  
Missing  1.7%  
Complete  97.8% 

 

 

Homology

Homology of the Malus x domestica Golden Delicious 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 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

Malus x domestica Golden Delicious v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) GoldenDelicious_NCBI_vs_arabidopsis.xlsx.gz
Malus x domestica v1.0 proteins with arabidopsis (Araport11) (FASTA file) GoldenDelicious_NCBI_vs_arabidopsis_hit.fasta.gz
Malus x domestica Golden Delicious v1.0 proteins without arabidopsis (Araport11) (FASTA file) GoldenDelicious_NCBI_vs_arabidopsis_noHit.fasta.gz
Malus x domestica v1.0 proteins with SwissProt homologs (EXCEL file) GoldenDelicious_NCBI_vs_swissprot.xlsx.gz
Malus x domestica Golden Delicious v1.0 proteins with SwissProt (FASTA file) GoldenDelicious_NCBI_vs_swissprot_hit.fasta.gz
Malus x domestica Golden Delicious v1.0 proteins without SwissProt (FASTA file) GoldenDelicious_NCBI_vs_swissprot_noHit.fasta.gz
Malus x domestica Golden Delicious v1.0 proteins with TrEMBL homologs (EXCEL file) GoldenDelicious_NCBI_vs_trembl.xlsx.gz
Malus x domestica Golden Delicious v1.0 proteins with TrEMBL (FASTA file) GoldenDelicious_NCBI_vs_trembl_hit.fasta.gz
Malus x domestica Golden Delicious v1.0 proteins without TrEMBL (FASTA file) GoldenDelicious_NCBI_vs_trembl_noHit.fasta.gz
Assembly

The Malus x domestica Golden Delicious NCBI genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes(FASTA file) Mdomestica_GoldenDelicious_NCBI_V1.fasta.gz
Gene Predictions

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

Downloads

Genes (GFF3 file) Mdomestica_GoldenDelicious_NCBI_V1.0.a1.genes.gff3.gz
Protein sequences (FASTA file) Mdomestica_GoldenDelicious_NCBI_V1.0.a1.pep.fasta.gz
CDS sequences (FASTA file) Mdomestica_GoldenDelicious_NCBI_V1.0.a1.cds.fasta.gz
Functional Analysis

Functional annotation for the Malus x domestica Golden Delicious genome v1.0 are available for download below. The Malus x domestica 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 GoldenDelicious_NCBI_genes2GO.xlsx.gz
IPR assignments from InterProScan GoldenDelicious_NCBI_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs GoldenDelicious_NCBI_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways GoldenDelicious_NCBI_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 Golden Delicious NCBI annotation. 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 GoldenDelicious_NCBI_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 GoldenDelicious_NCBI_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 GoldenDelicious_NCBI_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 GoldenDelicious_NCBI_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 GoldenDelicious_NCBI_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 GoldenDelicious_NCBI_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 GoldenDelicious_NCBI_pyrus_GDR_reftransV1