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New GS FLX Titanium Series Paired End Sequencing Improved De Novo Sequencing for High Quality Genome Assembly

Roche Applied Science has launched the latest update to the Genome Sequencer FLX System, the new GS FLX Titanium Library Paired End Adaptors for improved whole genome de novo sequencing. Widely recognized as the platform of choice for de novo sequencing applications, as a result of the system’s long shotgun reads, the addition of 3  kb, 8 kb and 20 kb span paired end libraries now facilitates assembly of increasingly complex genomes. The improved sequencing solution offers biologists more complete genome coverage, assembly into fewer, larger scaffolds and the ability to explore the full range of genetic variation.

De novo sequencing, which refers to the analysis of genomes without the use of a reference, has been largely enabled by the 454 Sequencing System, in recent years. Paired end reads (also known as “mate pair” reads) supplement shotgun reads to improve de novo assemblies, by completely or partially spanning highly repetitive genomics regions. Paired end reads aid in:

  • Ordering contigs into large scaffolds
  • Determining the sequence within large repeat regions
  • Identifying structural variations
  • Providing the complete genomic landscape, including gene order and operons


De novo sequencing and assembly of small genomes


The Genome Sequencer FLX System has accelerated the pace of discovery in diverse fields of biology. Researchers have published numerous studies demonstrating the system’s sequencing power to generate near-finished quality de novo assemblies of small genomes such as bacteria [1], viruses [2], and fungi [3]. With the launch of the GS FLX Titanium series paired end sequencing adaptors, multiple small genomes can be assembled from the data produced in a single instrument run (Table 1).

 

De novo sequencing and assembly of complex genomes


Until recently, the technical and economic constraints of the Sanger sequencing method limited the analysis of complex genomes. The Genome Sequencer FLX system has opened doors in a number of key research fields involving complex genomes, including plant and agricultural research and the study of endangered species. In the past year, researchers have published studies which report the comprehensive de novo sequencing of the salmon [4], rice [5], and salamander [6] genomes, among others. The improved GS FLX Titanium series paired end solution continues to raise the bar in de novo sequencing of complex genomes. The system’s 400-500 base shotgun reads and unique 20 kb span paired end reads ensure contiguous sequence information to cover the highly repetitive regions of complex genomes. The broad selection of insert lengths (3 kb, 8 kb, and 20 kb) means researchers can optimize project design according to the unique characteristics of any complex genome (Table 2).


For more information on the Genome Sequencer FLX System, please visit www.454.com.

References

  1. Tauch A et al. (2008) J Biotechnol 136(1-2):22-30
  2. La Scola B et al. (2008) Nature 455(7209):100-4
  3. Albert I et al. (2007) Nature 466(7135):572-6
  4. Quinn NL et al. (2008) BMC Genomics 9:404
  5. Rounsley S et al. (2009) Rice 2(1): 35-43
  6. Smith JJ et al. (2009) BMC Genomics 10:19


This article was originally published in Biochemica 3/2009, pages 7. ©Springer Medizin Verlag 2009

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