Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing
Abstract Background Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon ( Salmo salar ) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 4...
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ftdoajarticles:oai:doaj.org/article:7f674ba8a1e141369ef8b19cc31c97c5 2023-05-15T15:31:12+02:00 Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing Olafsdottir Gudbjorg Magnusdottir Steinunn de Leaniz Carlos Knox David Consuegra Sonia Bjornsdottir Snaedis Tompsett Scott Olafsson Kristinn Fridjonsson Olafur Verspoor Eric Hjorleifsdottir Sigridur 2011-04-01T00:00:00Z https://doi.org/10.1186/1471-2164-12-179 https://doaj.org/article/7f674ba8a1e141369ef8b19cc31c97c5 EN eng BMC http://www.biomedcentral.com/1471-2164/12/179 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-12-179 1471-2164 https://doaj.org/article/7f674ba8a1e141369ef8b19cc31c97c5 BMC Genomics, Vol 12, Iss 1, p 179 (2011) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2011 ftdoajarticles https://doi.org/10.1186/1471-2164-12-179 2022-12-31T04:34:43Z Abstract Background Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon ( Salmo salar ) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual. Results Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual. Conclusion The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species. Article in Journal/Newspaper Atlantic salmon North Atlantic Salmo salar Directory of Open Access Journals: DOAJ Articles Indel’ ENVELOPE(35.282,35.282,66.963,66.963) BMC Genomics 12 1 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Biotechnology TP248.13-248.65 Genetics QH426-470 Olafsdottir Gudbjorg Magnusdottir Steinunn de Leaniz Carlos Knox David Consuegra Sonia Bjornsdottir Snaedis Tompsett Scott Olafsson Kristinn Fridjonsson Olafur Verspoor Eric Hjorleifsdottir Sigridur Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon ( Salmo salar ) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual. Results Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual. Conclusion The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species. |
format |
Article in Journal/Newspaper |
author |
Olafsdottir Gudbjorg Magnusdottir Steinunn de Leaniz Carlos Knox David Consuegra Sonia Bjornsdottir Snaedis Tompsett Scott Olafsson Kristinn Fridjonsson Olafur Verspoor Eric Hjorleifsdottir Sigridur |
author_facet |
Olafsdottir Gudbjorg Magnusdottir Steinunn de Leaniz Carlos Knox David Consuegra Sonia Bjornsdottir Snaedis Tompsett Scott Olafsson Kristinn Fridjonsson Olafur Verspoor Eric Hjorleifsdottir Sigridur |
author_sort |
Olafsdottir Gudbjorg |
title |
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing |
title_short |
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing |
title_full |
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing |
title_fullStr |
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing |
title_full_unstemmed |
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing |
title_sort |
detection and mapping of mtdna snps in atlantic salmon using high throughput dna sequencing |
publisher |
BMC |
publishDate |
2011 |
url |
https://doi.org/10.1186/1471-2164-12-179 https://doaj.org/article/7f674ba8a1e141369ef8b19cc31c97c5 |
long_lat |
ENVELOPE(35.282,35.282,66.963,66.963) |
geographic |
Indel’ |
geographic_facet |
Indel’ |
genre |
Atlantic salmon North Atlantic Salmo salar |
genre_facet |
Atlantic salmon North Atlantic Salmo salar |
op_source |
BMC Genomics, Vol 12, Iss 1, p 179 (2011) |
op_relation |
http://www.biomedcentral.com/1471-2164/12/179 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-12-179 1471-2164 https://doaj.org/article/7f674ba8a1e141369ef8b19cc31c97c5 |
op_doi |
https://doi.org/10.1186/1471-2164-12-179 |
container_title |
BMC Genomics |
container_volume |
12 |
container_issue |
1 |
_version_ |
1766361699200270336 |