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Data Overview

Rosaceae Mapping Data

  • The peach genome sequence: The peach genome sequence version 1.0, was released April, 2010. It contains 28,692 putative protein coding genes.
     
  • Genetically Anchored Peach Physical Map: The latest peach physical map (Apr 2006) contains 18387 BACs and 1367 contigs. A total of 149 contigs are anchored to the TxE map.
     
  • Peach Transcriptome Map:  A total of 367 peach unigenes are anchored to genetic maps by hybridization to genetically anchored BACs. Of these, 216 unigenes are anchored to the TxE map. An additional 382 peach unigenes are anchored to genetic maps by hybridization to BACs that belong to genetically anchored BAC contigs.
     
  • Rosaceae Genetic Maps: Rosaceae genetic maps are available through CMap, the comparative map viewer. A total of over 1000 molecular markers and traits from various Rosaceae genetic maps and diversity studies are available from the marker or trait search page.
     
  • Data available for the three peach BACs that are completely sequenced: Anchored ESTs/markers and the sequences for the three BACs (082I18, 028F08 and pPn31C7) can be accessed from BAC search site. An online annotation pipeline is currently under development by the GDR team.
     

Rosaceae EST Data:

  • SNP Analysis: The publicly available autoSNP software was used to analyze the most recent versions of the Rosaceae unigene and the individual genera unigenes. A summary of the results and downloadable data can be found here. 
     
  • EST Assemblies: Assemblies of publicly available ESTs are available for the family Rosaceae and the genera Malus, Prunus, Fragaria, Rosa, Pyrus, and Rubus. Homology data for each assembly with SWISS-PROT is available to browse and download. Homology with the NCBI nr protein database and other rosaceae ESTs will be available soon.
     
  • EST Analysis: Full bioinformatics analysis, including quality trimming, assembly, homology searching, microsatellite discovery and putative unigene development, is currently available for Clemson Peach and Almond , UF Octoploid Strawberry, and CRA ISF Peach ESTs. Rose and blackberry projects will be available soon. 
     
 Organism  Project  EST Number
 Rosaceae  Rosaceae Assembly  359001
 Fragaria  Fragaria Assembly  49132
      x ananassa (octoploid strawberry)    
      whole plant:  Kevin Folta - University of Florida  1505
      vesca (diploid strawberry)    
      unopened flower buds:  Tom Davis - University of New Hampshire  2717
 Malus  Malus Assembly  249195
 Prunus  Prunus Assembly  89166
      amygdalus (almond)    
      developing seed:             Albert Abbott - Clemson University  2794
      persica (peach)    
      fruit mesocarp:  Albert Abbott - Clemson University  9984
      root:  Albert Abbott - Clemson University  Available Soon
      shoot:  Albert Abbott - Clemson University  7085
      fruit mesocarp:  Elisa Vendramin - CRA ISF  1667
 Rosa  Rosa Assembly  9077