The apple genome sequence and associated annotation are now available in GDR. Many thanks to Riccardo Velasco and his team for providing the data. 

While there are links in the text below, please go to the GDR home page (www.rosaceae.org) to access the data as the email links sometimes get re-routed incorrectly via the mail server at WSU.
Apple Genome v1.0

General Information

  • From this site 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.   
     

Important Details About This Assembly

  • Because of the heterozygous nature of the Malus x domestica genome, pseudomolecules corresponding to the chromosomes are not presented.   To preserve haplotype information, this assembly consists of sets of assembled contigs organized into metacontigs (clusters) and anchored to the chromosomes using 1,643 genetic markers.  There is no consensus sequence from assembled contigs.  Please see the whole genome publication in Nature Genetics for further details. 
     
  • Chromosomes are labeled 'chr1' through 'chr17' for each of the 17 chromosomes respectively.  Contigs from different haplotypes may align and overlap on the same chromosomal region.    Metacontigs that could not be anchored have been arranged sequentially in a chromosome-like feature named 'unanchored', however, the order of metacontigs on this "chromosome" is arbitrary.
     
  • Visualization of the genome using GBrowse orients the contigs within a chromosome, however, gene predictions, location of markers, tRNA and protein alignments were constructed and aligned using contig sequences.
     
  • 5' and 3' UTR regions are currently not available for gene models.
     

Data and Tools 

 
Dorrie Main, PhD
Associate Professor of Bioinformatics
Dept of Horticulture and Landscape Architecture
Washington State University
45 Johnson Hall, Pullman, WA 99164-6414
Email: dorrie@wsu.edu
Tel: (509) 335 2774
Fax: (509) 335 8690
URL: www.bioinfo.wsu.edu