PAG-XIV  Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA


Poster: Genome Sequencing & ESTs

P10

Plant Chromosome Mapping Strategies At The Wellcome Trust Sanger Institute

Christine Nicholson , Carol Scott , Sean Humphray , Jane Rogers

  Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

The NSF/EU Medicago truncatula Genome Sequencing Project (http://www.medicago.org/genome) and International Tomato Sequencing Project (http://www.sgn.cornell.edu/help/about/tomato_sequencing.html) are underway. The role of the Wellcome Trust Sanger Institute in these projects is to map and fully sequence the gene-space of Medicago truncatula chromosome 3 (38Mbp) and Tomato (Solanum lycopersicum) chromosome 4 (19Mbp). For both projects we have obtained raw fingerprint databases for each organism from UC Davis and Arizona Genomics Institute, respectively. These have been collated into distinct FPC (FingerPrintContig) databases for M. truncatula chromosome 3 and Tomato chromosome 4, that are being edited at Sanger. In silico analysis of both FPC databases is ongoing and all possible electronic contig merges for Medicago chromosome 3 and Tomato chromosome 4 have been made. Merges have taken into account marker data, BAC end sequences (BES) and other available sequence information. Our sequence BAC identification strategy entails selection of minimal tiling paths across the contigs of each chromosome. We aim to reduce the current contig numbers of 54 contigs on Medicago chromosome 3 and 55 on Tomato chromosome 4, by extending and bridging contigs. This will facilitate selection of longer tilepaths across the chromosomes, with smaller overlaps between neighbouring BACs in order to improve sequencing efficiency. Several approaches are underway to attempt to bridge gaps, including walking from contig ends by hybridization onto library filters. For Medicago, probes have been designed from BES or existing BAC sequences. In the case of Tomato, we will augment the fingerprint database with additional agarose gel fingerprints generated from the SL_MboI library. The Mapping and BAC selection strategies that are in place for these projects will be demonstrated.