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The Atlantic salmon genome provides insights into rediploidization.

ABSTRACT: The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

SUBMITTER: Lien S

PROVIDER: S-EPMC8127823 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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The Atlantic salmon genome provides insights into rediploidization.

Lien Sigbjørn S Koop Ben F BF Sandve Simen R SR Miller Jason R JR Kent Matthew P MP Nome Torfinn T Hvidsten Torgeir R TR Leong Jong S JS Minkley David R DR Zimin Aleksey A Grammes Fabian F Grove Harald H Gjuvsland Arne A Walenz Brian B Hermansen Russell A RA von Schalburg Kris K Rondeau Eric B EB Di Genova Alex A Samy Jeevan K A JK Olav Vik Jon J Vigeland Magnus D MD Caler Lis L Grimholt Unni U Jentoft Sissel S Våge Dag Inge DI de Jong Pieter P Moen Thomas T Baranski Matthew M Palti Yniv Y Smith Douglas R DR Yorke James A JA Nederbragt Alexander J AJ Tooming-Klunderud Ave A Jakobsen Kjetill S KS Jiang Xuanting X Fan Dingding D Hu Yan Y Liberles David A DA Vidal Rodrigo R Iturra Patricia P Jones Steven J M SJ Jonassen Inge I Maass Alejandro A Omholt Stig W SW Davidson William S WS

Nature 20160418 7602

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4 ...[more]

PMID: 27088604

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Project description:BackgroundIn a previous study, we found low persistence of linkage disequilibrium (LD) phase across breeding populations of Atlantic salmon. Accordingly, we observed no increase in accuracy from combining these populations for genomic prediction. In this study, we aimed to examine if the same were true for detection power in genome-wide association studies (GWAS), in terms of reduction in p-values, and if the precision of mapping quantitative trait loci (QTL) would improve from such analysis. Since individual records may not always be available, e.g. due to proprietorship or confidentiality, we also compared mega-analysis and meta-analysis. Mega-analysis needs access to all individual records, whereas meta-analysis utilizes parameters, such as p-values or allele substitution effects, from multiple studies or populations. Furthermore, different methods for determining the presence or absence of independent or secondary signals, such as conditional association analysis, approximate conditional and joint analysis (COJO), and the clumping approach, were assessed.ResultsMega-analysis resulted in increased detection power, in terms of reduction in p-values, and increased precision, compared to the within-population GWAS. Only one QTL was detected using conditional association analysis, both within populations and in mega-analysis, while the number of QTL detected with COJO and the clumping approach ranged from 1 to 19. The allele substitution effect and -log10p-values obtained from mega-analysis were highly correlated with the corresponding values from various meta-analysis methods. Compared to mega-analysis, a higher detection power and reduced precision were obtained with the meta-analysis methods.ConclusionsOur results show that combining multiple datasets or populations in a mega-analysis can increase detection power and mapping precision. With meta-analysis, a higher detection power was obtained compared to mega-analysis. However, care must be taken in the interpretation of the meta-analysis results from multiple populations because their test statistics might be inflated due to population structure or cryptic relatedness.

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The Atlantic salmon genome provides insights into rediploidization.

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The Atlantic salmon genome provides insights into rediploidization.

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