Friday, October 23, 2009
This Whole Genome Profiling map will be used as the scaffold to produce a superior tomato draft genome assembly by the end of this year.
Concluding a successful collaboration between Centre for BioSystems Genomics (CBSG) and the Crop Genome Center of KeyGene, KeyGene delivered a high quality sequence-based physical map of the tomato genome. The physical map was constructed using KeyGene proprietary Whole Genome Profiling (WGP) technology that is based on next generation sequencing of BAC clones pooled by our partner Amplicon Express. Assembly of the BAC clones under high stringency conditions covered the complete 950 Mb tomato genome. Details on the tomato physical map will be presented during the 6th Solanaceae Genome Workshop on November 8-13, 2009 in New Delhi, India.
As part of the collaboration CBSG together with several other partners of the International Sequencing Consortium SOL produced a high-coverage shot gun sequence of the tomato genome using the
next-generation sequencing platforms GS FLX Titanium (Roche) and SOLiD (Life Technologies). KeyGene’s WGP map will serve as a scaffold to anchor and order the sequence contigs produced by the
consortium. This is expected to yield a superior draft sequence of the tomato genome by the end of 2009.
Michiel van Eijk, Vice-President Upstream Research: ‘The WGP technology proves to be a a very powerfull technology to expedite genome assembly of complex plant genomes. Whole genome shotgun sequencing and the WGP technology turn out to be a cost effective combination to produce superior quality genome assemblies’.
Marco van Schriek, Team Leader of KeyGene’s Solanaceae group adds: ‘The tomato genome assembly will support our molecular breeding programs directly. A number of applications have already been developed using the insights we gained from the structure and sequence of the tomato genome’.
René Klein Lankhorst, coordinator of the EU-SOL Project: ‘We are very pleased with the result of the physical map. The aim of the SOL Consortium is to deliver a “gold standard” sequence of the tomato genome to the scientific community and the new physical map will be instrumental in reaching this goal’.
Roeland van Ham, coordinator of the international genome assembly effort: ‘We are thrilled with the quality of the WGP data, for which preliminary analysis indicate a very high overlap between WGP
sequence tags and shotgun contigs. We expect that full integration of the WGP map will set a new quality standard in draft genome sequencing’.