Feasibility of GS FLX Pyrosequencing for Atlantic Salmon Genome Sequencing
Author Information
Author(s): Nicole L. Quinn, Natasha Levenkova, William Chow, Pascal Bouffard, Keith A. Boroevich, James R. Knight, Thomas P. Jarvie, Krzysztof P. Lubieniecki, Brian A. Desany, Ben F. Koop, Timothy T. Harkins, William S. Davidson
Primary Institution: Simon Fraser University
Hypothesis
Can the GS FLX pyrosequencing system effectively sequence the complex genome of Atlantic salmon?
Conclusion
The study found that while GS FLX technology improved assembly, it is still limited for de novo sequencing of complex genomes, necessitating Sanger sequencing for a reference genome.
Supporting Evidence
- The GS FLX technology produced a comparable number of scaffolds to Sanger sequencing but with more gaps.
- The addition of paired end reads significantly improved the assembly quality.
- The study confirmed the utility of GS FLX for gene discovery despite its limitations.
Takeaway
The researchers tried a new method to read the DNA of Atlantic salmon, and while it worked better than before, they still need to use an older method for the best results.
Methodology
The study used GS FLX pyrosequencing and Sanger sequencing to analyze a 1 Mb region of the Atlantic salmon genome.
Limitations
The GS FLX assemblies had numerous gaps, particularly in repetitive regions, making them less complete than Sanger assemblies.
Digital Object Identifier (DOI)
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