| Abstract Detail
Tomato sequencing - Morning Nicholson, Christine [1], McLaren, Karen [1], Scott, Carol [1], Sims, Sarah [1], Beasley, Helen [1], Bishop, Gerard [2], Seymour, Graham [3], Bryan, Glenn [4], Humphray, Sean [1], Rogers, Jane [1]. Mapping, Sequencing and Finishing the Gene Space of Solanum lycopersicum Chromosome 4. THE Wellcome Trust Sanger Institute is mapping, sequencing and finishing the estimated 19Mb of gene space on Tomato (Solanum lycopersicum) chromosome 4. The project is funded by the BBSRC and is part of the International Tomato Sequencing Project (http://www.sgn.cornell.edu/help/about/tomato_sequencing.html). Our clone-by-clone sequencing strategy commences with a tile path of minimally overlapping clones that is selected using both fingerprint and BAC end sequence (BES) information. The initial fingerprint map was constructed from the LE_HBa library at The Arizona Genomics Institute and assembled into an FPC (FingerPrintContig) database. It currently represents approximately 10X coverage. Chromosome 4 contigs were identified from overgo analysis conducted at Cornell and these have been evaluated in silico. After all possible electronic merges 58 contigs are assigned to chromosome 4. We are currently augmenting the map by fingerprinting the SL_MboI library, reproducing the original agarose gel protocol to enable comparison and integration of the two datasets. The additional fingerprints will make the clones “visible” in FPC and the data will be available to the community. The average insert size of the SL_MboI BACs (135kb) is larger than the LE_HBa BACs (117kb) and once fingerprinted, may provide more efficient substrates for sequencing as well as closing gaps between physical map contigs. DNA is prepared from single colony isolates and undergoes fingerprint verification. The DNA is sequenced using Applied Biosystems Big Dye Terminator chemistry and the data analysed on AB 3730 automated sequencing instruments. Clone sequences are edited and correctly re-assembled to HTGS Phase 3 standard using GAP4 (Staden) combined with customised software tools. All data are released into the public domain throughout the process: sequence traces are uploaded to the Ensembl and GenBank trace archives, and clone sequences are deposited in the appropriate HTGS divisions of EMBL, GenBank & DDBJ.
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Related Links:
International Tomato Sequencing Project
1 - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
2 - Imperial College London, Division of Biology, Wye Campus, Wye , Ashford,, TN25 5AH, United Kindom
3 - University of Warwick, Warwick HRI, Wellesbourne, CV35 9EF, United Kindom
4 - Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
Keywords:
tomato
Chromosome 4
mapping
sequencing
Finishing.
Session: SAT04-5
Location: Hall of Ideas Room E/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 9:15 AM
Abstract ID:329 |
