[GDR] apple genome sequence and annotation available on GDR

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 http://www.rosaceae.org/projects/apple_genome#publication 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 http://www.rosaceae.org/gb/gbrowse/malus_x_domestica 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

* Apple Genome Sequence

* View the Apple v1.0 genome assembly and annotations in GBrowse http://www.rosaceae.org/gb/gbrowse/malus_x_domestica * Download the Malus x domestica genome contigs http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.contigs.fa.gz (fasta, 278 MB compressed) * Download the Malus x domestica chloroplast sequence http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.chloroplast.fa.gz (fasta, 50 KB compressed) * Download the Malus x domestica mitochondrial sequence http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.mitochondria.fa.gz (fasta, 126KB compressed)

* Apple Genome Sequence Predicted Genes

* Download the predicted consensus gene set CDS sequences http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.consensus_CDS.fa.gz (fasta, 18 MB compressed) * Download the predicted consensus gene set peptides sequences http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.consensus_peptide.fa.gz (fasta, 12 MB compressed) * Download other gene prediction CDS sequences http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.other_CDS.fa.gz (fasta, 78 MB compressed) * Download other gene prediction peptides sequences http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.other_peptide.fa.gz (fasta, 49 MB compressed)

* Predicted Gene Function

* Download the non-redundant, best-match predicted protein homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_function_101210.formated.xls (excel, 59 MB) * Download species/database specific protein homologs:

* 71,657 apple gene peptides with Arabidopsis homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_tair_blasp_100510.formated.xls (excel, 78 MB) * 71,245 apple gene peptides with Swiss-Prot homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_uniprot_sprot_blastp_100610.formated.xls (excel, 54 MB) * 84,380 apple gene peptides with TrEMBL homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_uniprot_trembl_blastp_100610.formated.xls (excel, 68 MB) * 73,479 apple gene peptides with Grape homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_Vitis_tblastn_100610.formated.xls (excel, 62 MB) * 78,017 apple gene peptides with Peach homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_peach_blastp_100610.formated.xls (excel, 66 MB) * 79,527 apple gene peptides with Poplar homologs http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene_pep_poplar_blastp_100610.formated.xls (excel, 69 MB)

* BLAST your sequences

* using the GDR NCBI BLAST Server http://www.rosaceae.org/bio/content?title=&url=http://app.bioinfo.wsu.edu/blast/blast_noheader.html&style=width:950px;height:950px; - results returned to your screen * using the GDR BATCH BLAST Server http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_blast - upload many sequences and have the results parsed out in an excel file

* Markers

* Download the apple markers with links to GBrowse & CMAP http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.markers.xls

* Questions or Comments?

* Contact us with questions/feedback/comments (select the apple genome in the dropdown box in the contact form http://www.rosaceae.org/contact )

* Whole Genome Publication

* Riccardo Velasco , Andrey Zharkikh , Jason Affourtit , Amit Dhingra , Alessandro Cestaro , Ananth Kalyanaraman , Paolo Fontana , Satish K Bhatnagar , Michela Troggio , Dmitry Pruss , Silvio Salvi , Massimo Pindo , Paolo Baldi , Sara Castelletti , Marina Cavaiuolo , Giuseppina Coppola , Fabrizio Costa , Valentina Cova , Antonio Dal Ri , Vadim Goremykin , Matteo Komjanc , Sara Longhi , Pierluigi Magnago , Giulia Malacarne , Mickael Malnoy , Diego Micheletti , Marco Moretto , Michele Perazzolli , Azeddine Si-Ammour , Silvia Vezzulli , Elena Zini , Glenn Eldredge , Lisa M Fitzgerald , Natalia Gutin , Jerry Lanchbury , Teresita Macalma , Jeff T Mitchell , Julia Reid , Bryan Wardell , Chinnappa Kodira , Zhoutao Chen , Brian Desany , Faheem Niazi , Melinda Palmer , Tyson Koepke , Derick Jiwan begin_of_the_skype_highlighting end_of_the_skype_highlighting , Scott Schaeffer, Vandhana Krishnan , Changjun Wu , Vu T Chu , Stephen T King , Jessica Vick , Quanzhou Tao , Amy Mraz , Aimee Stormo , Keith Stormo , Robert Bogden , Davide Ederle , Alessandra Stella , Alberto Vecchietti , Martin M Kater , Simona Masiero , Pauline Lasserre , Yves Lespinasse , Andrew C Allan , Vincent Bus , David Chagné , Ross N Crowhurst , Andrew P Gleave , Enrico Lavezzo , Jeffrey A Fawcett , Sebastian Proost , Pierre Rouzé , Lieven Sterck , Stefano Toppo , Barbara Lazzari , Roger P Hellens , Charles-Eric Durel , Alexander Gutin , Roger E Bumgarner , Susan E Gardiner , Mark Skolnick , Michael Egholm , Yves Van de Peer , Francesco Salamini & Roberto Viola. The Genome of the Domesticated Apple (Malus x domestica Borkh.) http://dev.rosaceae.org/bio/content/?title=&url=http://www.rosaceae.org/cgi-bin/gdr/gdr_publication.cgi?pub_id=4451&style=width:940px;height:950px; Nature Genetics 42, 833-839. 2010.

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 http://www.bioinfo.wsu.edu/