An apple genome sequencing initiative

Dhingra, Amit; Schaeffer, Scott; Koepke, Tyson; Jiwan, Derick; Krishnan, Vandhana; Wu, Changjun; Kalyanaraman, Ananth; Bumgarner, Roger; Durel, Charles Eric; Chevreau, Elisabeth,; Lespinasse, Yves; Velasco, Riccardo; Rees, Jasper; Rokhsar, Dan; Bogden, Robert

An apple genome sequencing initiative

2010

Apple is a unique biological system belonging to Rosaceae, a family representing several important fruit and flower crops. In order to gain a holistic understanding of the structure and function of its genes, we have initiated sequencing of the apple genome. Our approach employs sequencing of a genetically simpler double haploid Golden Delicious apple and is based on obtaining de-novo draft genome assemblies by largely utilizing next-generation sequencing approaches. We have generated a 6X BAC library of the Double Haploid Apple. The genomic scaffold will be generated via directed sequencing of 27,000 BAC ends using 454 Titanium. The data will be utilized for genome assembly as well as organizing the BACs into a minimal tiling path using custom computational tools. Additional Scaffold will be generated by end-sequencing of 10,000 BACs. The resulting scaffold will be utilized to perform de-novo assembly of the apple genome utilizing over 4X shotgun coverage of the complex genome obtained with the GS FLX platform. This information is expected to serve as a foundation for developing healthier, value-added and nutritionally enhanced apple varieties for the public. This research is also expected to create educational, training and outreach avenues for undergraduate students, graduate students and the general public in the area of horticultural genomics.

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