Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes
Abstract Background Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencin...
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ftdoajarticles:oai:doaj.org/article:f221de54a46b449184655cd7a5e6f212 2023-05-15T15:31:14+02:00 Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes Primmer Craig R Ryynänen Heikki J 2006-07-01T00:00:00Z https://doi.org/10.1186/1471-2164-7-192 https://doaj.org/article/f221de54a46b449184655cd7a5e6f212 EN eng BMC http://www.biomedcentral.com/1471-2164/7/192 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-7-192 1471-2164 https://doaj.org/article/f221de54a46b449184655cd7a5e6f212 BMC Genomics, Vol 7, Iss 1, p 192 (2006) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2006 ftdoajarticles https://doi.org/10.1186/1471-2164-7-192 2022-12-31T04:22:23Z Abstract Background Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencing projects in several fish species have provided a vast amount of data in public databases, which can be utilized in novel SNP discovery in salmonids. However, the suggested duplicated nature of the salmonid genome may hamper SNP characterization if the primers designed in conserved gene regions amplify multiple loci. Results Here we introduce a new intron-primed exon-crossing (IPEC) method in an attempt to overcome this duplication problem, and also evaluate different priming methods for SNP discovery in Atlantic salmon ( Salmo salar ) and other salmonids. A total of 69 loci with differing priming strategies were screened in S. salar , and 27 of these produced ~13 kb of high-quality sequence data consisting of 19 SNPs or indels (one per 680 bp). The SNP frequency and the overall nucleotide diversity (3.99 × 10 -4 ) in S. salar was lower than reported in a majority of other organisms, which may suggest a relative young population history for Atlantic salmon. A subset of primers used in cross-species analyses revealed considerable variation in the SNP frequencies and nucleotide diversities in other salmonids. Conclusion Sequencing success was significantly higher with the new IPEC primers; thus the total number of loci to screen in order to identify one potential polymorphic site was six times less with this new strategy. Given that duplication may hamper SNP discovery in some species, the IPEC method reported here is an alternative way of identifying novel polymorphisms in such cases. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles BMC Genomics 7 1 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Biotechnology TP248.13-248.65 Genetics QH426-470 Primmer Craig R Ryynänen Heikki J Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencing projects in several fish species have provided a vast amount of data in public databases, which can be utilized in novel SNP discovery in salmonids. However, the suggested duplicated nature of the salmonid genome may hamper SNP characterization if the primers designed in conserved gene regions amplify multiple loci. Results Here we introduce a new intron-primed exon-crossing (IPEC) method in an attempt to overcome this duplication problem, and also evaluate different priming methods for SNP discovery in Atlantic salmon ( Salmo salar ) and other salmonids. A total of 69 loci with differing priming strategies were screened in S. salar , and 27 of these produced ~13 kb of high-quality sequence data consisting of 19 SNPs or indels (one per 680 bp). The SNP frequency and the overall nucleotide diversity (3.99 × 10 -4 ) in S. salar was lower than reported in a majority of other organisms, which may suggest a relative young population history for Atlantic salmon. A subset of primers used in cross-species analyses revealed considerable variation in the SNP frequencies and nucleotide diversities in other salmonids. Conclusion Sequencing success was significantly higher with the new IPEC primers; thus the total number of loci to screen in order to identify one potential polymorphic site was six times less with this new strategy. Given that duplication may hamper SNP discovery in some species, the IPEC method reported here is an alternative way of identifying novel polymorphisms in such cases. |
format |
Article in Journal/Newspaper |
author |
Primmer Craig R Ryynänen Heikki J |
author_facet |
Primmer Craig R Ryynänen Heikki J |
author_sort |
Primmer Craig R |
title |
Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes |
title_short |
Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes |
title_full |
Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes |
title_fullStr |
Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes |
title_full_unstemmed |
Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes |
title_sort |
single nucleotide polymorphism (snp) discovery in duplicated genomes: intron-primed exon-crossing (ipec) as a strategy for avoiding amplification of duplicated loci in atlantic salmon ( salmo salar ) and other salmonid fishes |
publisher |
BMC |
publishDate |
2006 |
url |
https://doi.org/10.1186/1471-2164-7-192 https://doaj.org/article/f221de54a46b449184655cd7a5e6f212 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
BMC Genomics, Vol 7, Iss 1, p 192 (2006) |
op_relation |
http://www.biomedcentral.com/1471-2164/7/192 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-7-192 1471-2164 https://doaj.org/article/f221de54a46b449184655cd7a5e6f212 |
op_doi |
https://doi.org/10.1186/1471-2164-7-192 |
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BMC Genomics |
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7 |
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1 |
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1766361733949030400 |