Apple genome sequencing initiative
The blueprint for all biological processes in an apple is coded by its genome. However, due to its enormous size and complexity it is impossible to access this information all at once. The information can only be accessed in small increments, which necessitates piecing together the fragmented information. To solve the genomic puzzle of the apple we plan to capture its genome in about 37,000 manageable pieces called BAC clones. Each clone covers about 120,000 nucleotides each. In order to fit the genomic pieces in a continuum we plan to access the sequence information available at either end of these pieces and arrange them linearly to serve as a “scaffold”.
Our laboratory has an ongoing complementary project to generate apple genome sequence information in even shorter increments of about 250 nucleotides each. The scaffold will serve as a foundation to “hang” millions of such smaller pieces and enable resurrection of the apple genome in its entirety. This information is expected to serve as a foundation for developing healthier, value-added, and nutritionally enhanced apple varieties for the public. Since these apples belong to the Rosaceae family of apples this research is expected to enable improvements in other members of the family as well.
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. Overall, this research is expected to facilitate development of novel apple varieties that will sustain the US apple industry in the face of ever-changing economic and environmental scenarios.
Objective 1. Develop an apple genome “scaffold”
A genome scaffold is vital for de-novo assembly of shotgun reads obtained from 454 technology and other high-throughput sequencing strategies like Solexa and ABI SOLiD. We propose to develop a 6X BAC library from a genetically simpler double haploid (DH) apple (Lespinasse et al., 1999).
The research community has open access to the 6.5X DH apple BAC library generated with support from USDA-NRI program. The BAC library is available in the following formats:
a) Quality Controlled copy of the DH apple BAC library**,
b) Nylon Filters for screening the apple library by DNA/DNA hybridization,
c) Library Screening Services for this library- researchers would provide ~1Kb to 2 Kb of genomic DNA sequence data from each region of interest.
d) Specific BAC clones from the apple library.
To obtain a quote or technical discussions regarding the library, please contact:
Robert Bogden (bogden at genomex.com)
Phone: 1-509-432-9555 or 1-509-332-8080.
(**The double haploid (DH) genotype used to construct the BAC library was bred at INRA, Angers, France, by Y. Lespinasse et al.Acta Hort. 1999 after duplication of an haploid individual selected in the progeny of a selfed derivative from the cultivar ‘Golden Delicious’)
End sequencing of 36,864 BACs will facilitate development of a genome scaffold for assembling the shotgun sequences, complementing the 4X genome coverage, that is being generated under the aegis of the public initiative for apple genome sequencing that we recently initiated with support from WSU and Washington Tree Fruit Research Commission.
Objective 2. Develop a publicly-accessible computational framework for the apple genome sequencing project.
The preliminary sequence information from the double haploid apple is being assembled and annotated using open-source bioinformatics modules available from www.GMOD.org and locally hosted on a Linux based server in the lab.
We propose to expand the current pipeline to enhance its function for genome assembly purposes and make it publicly accessible via the laboratory web portal and other public databases like NCBI.