Malus x domestica Whole Genome v1.0 Assembly & Annotation
| Analysis Name | Malus x domestica Whole Genome v1.0 Assembly & Annotation |
|---|---|
| Software | Constructed using a gene-centered strategy |
| Source | Sanger reads |
| Date performed | 2012-07-26 |
| Materials & Methods | From this page you can browse and download the whole genome sequence of the Velaso et al., 2010 published apple genome assembly v1.0; predicted gene transcripts, their locations and putative function based on homology to known genes. You can BLAST your sequences against the genome sequence, the predicted genes and associated transcripts. You can search and browse the chromosomes, predicted genes and markers in GBrowse and view the evidence for each prediction and feature. There are two asemblies currently available The original contig-based assembly from the Velaso et al., 2010 publication
Reference Velasco et. al. The genome of the domesticated apple (Malus × domestica Borkh). Nature Genetics 42, 833–839 (2010) Questions or Comments? Contact us with questions/feedback/comments (select the apple genome in the dropdown box in the contact form). Is your questions already answered on the Apple Genome v1.0 Frequently Asked Questions (FAQ) page? |
The Malus x domestica v1.0 genome assembly files are available in FASTA and GFF3 formats. There are no pseudomolecule (chromosome) sequence files available for this assembly because of the multiple haplotypes present in the assembly. Please see the Malus x domestica v1.0 pseudo haplotype (primary assembly) for a pseudomolecule sequence.
Downloads
| Contigs (FASTA file) | Malus_x_domestica.v1.0.contigs.fa.gz |
| Contigs (GFF3 file) | Malus_x_domestica.v1.0.contigs.gff.gz |
| Chloroplast (FASTA file) | Malus_x_domestica.v1.0.chloroplast.fa.gz |
| Mitochondria (FASTA file) | Malus_x_domestica.v1.0.mitochondria.fa.gz |
Gene Predictions
Gene models were predicted on the assembly contigs using various gene prediction tools such as Glimmer, FGENESH, Genewise, GMAP and Twinscan. A final consensus gene set was constructed using evidence derived from all of these gene prediction tools. Both the consensus sequences and alternate gene models are available for download below. The consensus genes have been mapped to chromosomal positions. However this is for convinence as there is no chromosomal sequence for this assembly.
5' and 3' UTR regions are currently not available for gene models
Downloads
| Consensus gene model CDSs (FASTA) | Malus_x_domestica.v1.0.consensus_CDS.fa.gz |
| Consensus gene model CDSs with 300bp flanking (FASTA) | Malus_x_domestica_v1.0.consensus_CDS300flanking.fa.gz |
| Consensus gene model proteins (FASTA) | Malus_x_domestica.v1.0.consensus_peptide.fa.gz |
| Alternate gene model CDSs (FASTA) | Malus_x_domestica.v1.0.other_CDS.fa.gz |
| Alternate gene model proteins (FASTA) | Malus_x_domestica.v1.0.other_peptide.fa.gz |
| Consensus genes located on chromosomes (GFF3) | Malus_x_domestica.v1.0.consensus.gff.gz |
| Consensus genes located on contigs (GFF3) | Malus_x_domestica.v1.0.consensus2contigs.gff.gz |
The following functional annotation files were derived from processing all predicted consensus genes through InterProScan and the KEGG KAAS services. Genes are mapped to InterPro domains, GO terms, KEGG pathways and orthologs.
Downloads
| Consensus genes mapped to InterPro domains | Malus_x_domestica_v1.0.genes2IPR.txt |
| Consensus genes mapped to GO terms | Malus_x_domestica_v1.0.genes2GO.txt |
| Consensus genes mapped to KEGG pathways | Malus_x_domestica.v1.0.genes2KEGG_pathways.txt |
| Consensus genes mapped to KEGG orthologs | Malus_x_domestica.v1.0.genes2KEGG_orthologs.txt |
Excel Reports
Best hit reports of blastp of Malus x domestica genome v1.0 proteins versus various protein databases are available below in Excel format.
Downloads
| Non-redundant best-match proteins (Excel file) | Malus_x_domestica.v1.0_gene_pep_function_101210.formated.xls |
| TAIR (arabidopsis) (Excel file) | Malus_x_domestica.v1.0_gene_pep_tair_blasp_100510.formated.xls |
| ExPASy TrEMBL (Excel file) | Malus_x_domestica.v1.0_gene_pep_uniprot_trembl_blastp_100610.formated.xls |
| ExPASy SwissProt (Excel file) | Malus_x_domestica.v1.0_gene_pep_uniprot_sprot_blastp_100610.formated.xls |
| Prunus persica (peach) v1.0 proteins (Excel file) | Malus_x_domestica.v1.0_gene_pep_peach_blastp_100610.formated.xls |
| Populus trichocarpa (poplar) v2.0 proteins (Excel file) | Malus_x_domestica.v1.0_gene_pep_poplar_blastp_100610.formated.xls |
| Vitis vinifera (grape) proteins (Excel file) | Malus_x_domestica.v1.0_gene_pep_Vitis_tblastn_100610.formated.xls |
Markers such as SNPs, SSRs, ESTs, etc are available for download in Excel and tab-delimited format.
Downloads
Repeats were predicted using read depth information from the genome assembly and then mapped for convienence to chromosomal positions. Both mappings are available in GFF file below.
Downloads
| Predicted repeats aligned to chromosomes (GFF file) | Malus_x_domestica.v1.0.repeats.gff.gz |
| Predicted repeats aligned to contigs (FASTA file) | Malus_x_domestica.v1.0.repeats.fa.gz |
| Predicted repeats aligned to contigs (GFF file) | Malus_x_domestica.v1.0.repeats2contigs.gff.gz |
All assembly and annotation files are available for download by selecting the desired data type in the right-hand "Resources" side bar. Each data type page will provide a description of the available files and links do download.
