Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome
BioMed Central Background: 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 surprisi...
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ftuvicpubl:oai:dspace.library.uvic.ca:1828/5547 2023-05-15T15:31:14+02:00 Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome Quinn, Nicole L Levenkova, Natasha Chow, William Bouffard, Pascal Boroevich, Keith A Knight, James R Jarvie, Thomas P Lubieniecki, Krzysztof P Desany, Brian A Koop, Ben F Harkins, Timothy T Davidson, William S 2008 application/pdf http://hdl.handle.net/1828/5547 http://www.biomedcentral.com/1471-2164/9/404 https://doi.org/10.1186/1471-2164-9-404 en eng BioMed Central Quinn et al.: Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9:404. http://www.biomedcentral.com/1471-2164/9/404 http://dx.doi.org/10.1186/1471-2164-9-404 http://hdl.handle.net/1828/5547 Article 2008 ftuvicpubl https://doi.org/10.1186/1471-2164-9-404 2022-05-19T06:11:56Z BioMed Central Background: 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 ... Article in Journal/Newspaper Atlantic salmon Salmo salar University of Victoria (Canada): UVicDSpace BMC Genomics 9 1 404 |
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Open Polar |
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University of Victoria (Canada): UVicDSpace |
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ftuvicpubl |
language |
English |
description |
BioMed Central Background: 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 ... |
format |
Article in Journal/Newspaper |
author |
Quinn, Nicole L Levenkova, Natasha Chow, William Bouffard, Pascal Boroevich, Keith A Knight, James R Jarvie, Thomas P Lubieniecki, Krzysztof P Desany, Brian A Koop, Ben F Harkins, Timothy T Davidson, William S |
spellingShingle |
Quinn, Nicole L Levenkova, Natasha Chow, William Bouffard, Pascal Boroevich, Keith A Knight, James R Jarvie, Thomas P Lubieniecki, Krzysztof P Desany, Brian A Koop, Ben F Harkins, Timothy T Davidson, William S Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome |
author_facet |
Quinn, Nicole L Levenkova, Natasha Chow, William Bouffard, Pascal Boroevich, Keith A Knight, James R Jarvie, Thomas P Lubieniecki, Krzysztof P Desany, Brian A Koop, Ben F Harkins, Timothy T Davidson, William S |
author_sort |
Quinn, Nicole L |
title |
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome |
title_short |
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome |
title_full |
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome |
title_fullStr |
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome |
title_full_unstemmed |
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome |
title_sort |
assessing the feasibility of gs flx pyrosequencing for sequencing the atlantic salmon genome |
publisher |
BioMed Central |
publishDate |
2008 |
url |
http://hdl.handle.net/1828/5547 http://www.biomedcentral.com/1471-2164/9/404 https://doi.org/10.1186/1471-2164-9-404 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Quinn et al.: Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9:404. http://www.biomedcentral.com/1471-2164/9/404 http://dx.doi.org/10.1186/1471-2164-9-404 http://hdl.handle.net/1828/5547 |
op_doi |
https://doi.org/10.1186/1471-2164-9-404 |
container_title |
BMC Genomics |
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9 |
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1 |
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404 |
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1766361731412525056 |