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- Ulrich Schwoerer
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454 Sequencing Systems Enable High Quality De Novo Assembly of Oil Palm Genome
While the completion of the 1.7 billion base pair oil palm genome is an important agricultural milestone, it also signals a fundamental shift in the technological approach used for sequencing of large complex plant genomes. The genome was sequenced using only the Genome Sequencer FLX Titanium system and then assembled and analyzed by Synamatix, a leading bioinformatics company based in Malaysia. Importantly, this is the first de novo genome assembly of a large and highly complex plant to be completed without the addition of conventional Sanger sequencing data. This fast and economical approach opens new doors to understanding the genetic makeup of a wide range of economically important plants, where sequencing has traditionally been prohibitively expensive.
"The resulting assembly has exceeded our expectations. By using the combination of long 454 reads and our own assembly pipeline, we were able to achieve a very high quality assembly in spite of the genome's very high repeat content. The approach we have taken for sequencing and assembly of the oil palm offers a significantly faster and more economical way to characterize large, highly complex genomes," said Robert Hercus, Synamatix Managing Director.
"We are proud to be part of this pivotal plant genomics project," said Michael Egholm, Chief Technology Officer and Vice President of Research and Development at 454 Life Sciences. "With the ability to generate millions of long, clonal reads, the 454 Sequencing system is an ideal tool for tackling highly complex plant genomes. We look forward to continue working with our bioinformatics partner, Synamatix, to sequence and assemble other commercially important plants."
454 Life Sciences, a center of excellence of Roche Applied Science, develops and commercializes the innovative 454 Sequencing System for ultra-high-throughput DNA sequencing. Specific applications include de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest. The hallmarks of the 454 Sequencing System are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired-end reads. The technology of the 454 Sequencing System has enabled hundreds of peer-reviewed studies in diverse research fields, such as cancer and infectious disease research, drug discovery, marine biology, anthropology, paleontology and many more.
Synamatix Sdn Bhd is a privately held company whose primary activities are R&D in bioinformatics and genomics. The company was founded in 2001 by Robert Hercus and initially focused on new approaches for the management, integration and analysis of large genomics data sets. The current phase of technology and product development is heavily geared towards the analysis of data from next-generation DNA sequencers and application of the results for medical, agricultural and synthetic fuel research. Synamatix has a growing number of clients and partners in the USA, Europe, Asia and Australia.
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The 454 GS FLX System is sold for life science research use only.
454, 454 SEQUENCING, 454 LIFE SCIENCES and GS FLX TITANIUM are trademarks of Roche.
Other brands or product names are trademarks of their respective holders.
Roche Diagnostics Deutschland GmbH
In 2008, Roche had over 80,000 employees worldwide and invested almost 9 billion Swiss francs in R&D. The Group posted sales of 45.6 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan. For more information: www.roche.com.
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