Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome

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dc.contributor.authorQuinn, Nicole L
dc.contributor.authorLevenkova, Natasha
dc.contributor.authorChow, William
dc.contributor.authorBouffard, Pascal
dc.contributor.authorBoroevich, Keith A
dc.contributor.authorKnight, James R
dc.contributor.authorJarvie, Thomas P
dc.contributor.authorLubieniecki, Krzysztof P
dc.contributor.authorDesany, Brian A
dc.contributor.authorKoop, Ben F
dc.contributor.authorHarkins, Timothy T
dc.contributor.authorDavidson, William S
dc.date.accessioned2014-08-11T22:38:24Z
dc.date.available2014-08-11T22:38:24Z
dc.date.copyright2008en_US
dc.date.issued2008-08-28
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: With a whole genome duplication event and wealth of biological data, salmonids are excellent model organisms for studying evolutionary processes, fates of duplicated genes and genetic and physiological processes associated with complex behavioral phenotypes. It is surprising therefore, that no salmonid genome has been sequenced. Atlantic salmon (Salmo salar) is a good representative salmonid for sequencing given its importance in aquaculture and the genomic resources available. However, the size and complexity of the genome combined with the lack of a sequenced reference genome from a closely related fish makes assembly challenging. Given the cost and time limitations of Sanger sequencing as well as recent improvements to next generation sequencing technologies, we examined the feasibility of using the Genome Sequencer (GS) FLX pyrosequencing system to obtain the sequence of a salmonid genome. Eight pooled BACs belonging to a minimum tiling path covering ~1 Mb of the Atlantic salmon genome were sequenced by GS FLX shotgun and Long Paired End sequencing and compared with a ninth BAC sequenced by Sanger sequencing of a shotgun library. Results: An initial assembly using only GS FLX shotgun sequences (average read length 248.5 bp) with ~30× coverage allowed gene identification, but was incomplete even when 126 Sanger-generated BAC-end sequences (~0.09× coverage) were incorporated. The addition of paired end sequencing reads (additional ~26× coverage) produced a final assembly comprising 175 contigs assembled into four scaffolds with 171 gaps. Sanger sequencing of the ninth BAC (~10.5× coverage) produced nine contigs and two scaffolds. The number of scaffolds produced by the GS FLX assembly was comparable to Sanger-generated sequencing; however, the number of gaps was much higher in the GS FLX assembly. Conclusion: These results represent the first use of GS FLX paired end reads for de novo sequence assembly. Our data demonstrated that this improved the GS FLX assemblies; however, with respect to de novo sequencing of complex genomes, the GS FLX technology is limited to gene mining and establishing a set of ordered sequence contigs. Currently, for a salmonid reference sequence, it appears that a substantial portion of sequencing should be done using Sanger technology.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipFunding for cGRASP (Consortium for Genomic Research on All Salmonids Project) was provided by Genome Canada and Genome BCen_US
dc.identifier.citationQuinn et al.: Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9:404.en_US
dc.identifier.urihttp://www.biomedcentral.com/1471-2164/9/404
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-9-404
dc.identifier.urihttp://hdl.handle.net/1828/5547
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.titleAssessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genomeen_US
dc.typeArticleen_US

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