Wageningen, The Netherlands
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 CBSG (Centre for BioSystems Genomics) 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 shotgun 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 very powerful 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’.

KeyGene is a R&D company with the mission to be the leading company in developing and applying DNA expertise in the field of molecular genetics with a focus on crop plants. KeyGene’s up to date R&D facilities with next generation sequencing platforms, an extensive computational infrastructure and long experience in working with plant genomes form the firm basis of the Crop Genome Center, which focuses on the development of high quality genome assemblies of 6F crops. KeyGene exploits its proprietary technologies, databases and know-how through strategic alliances, contract research and products for applications in the plant breeding industry. KeyGene has its headquarters in Wageningen, The Netherlands, a subsidiary in Rockville Maryland, USA and a Joint Lab at the Shanghai Institute of Biological Sciences in Shanghai, China.

The Centre for BioSystems Genomics (CBSG) is the Dutch National Centre for plant genomics research funded by the Netherlands Genomics Initiative as well as by its 15 private and 7 public partners. CBSG works at the forefront of the development and application of novel genome-based strategies for crop improvement.

Website: http://www.keygene.com

Published: October 23, 2009