Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing

Olafur Fridjonsson, Kristinn Olafsson, Scott Tompsett, Snaedis Bjornsdottir, Sonia Consuegra, David Knox, Carlos Garcia de Leaniz, Steinunn Magnusdottir, Gudbjorg Olafsdottir, Eric Verspoor, Sigridur Hjorleifsdottir

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12 Citations (Scopus)

Abstract

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.
Original languageEnglish
JournalBMC Genomics
Volume12
DOIs
Publication statusPublished - 7 Apr 2011

Cite this

Fridjonsson, O., Olafsson, K., Tompsett, S., Bjornsdottir, S., Consuegra, S., Knox, D., de Leaniz, C. G., Magnusdottir, S., Olafsdottir, G., Verspoor, E., & Hjorleifsdottir, S. (2011). Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing. BMC Genomics, 12. https://doi.org/10.1186/1471-2164-12-179