DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species

Laporte, Martin; Luyer, Jérémy Le; Rougeux, Clément; Dion-Côté, Anne-Marie; Krick, Madoka V.; Bernatchez, Louis

doi:10.1126/sciadv.aaw1644

Cited by 52 publications

(60 citation statements)

References 48 publications

(85 reference statements)

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“…47 . As work in other taxa has revealed that transposon polymorphisms contribute to adaptive evolution 48,49 and speciation 50 , future studies on pTSsa2 should investigate such possibilities in Salmo. We also showed that Atlantic salmon deletion SVs are more likely to overlap genes retained as ohnolog pairs from the Ss4R WGD event compared to singleton genes, and demonstrate SV overrepresentation in ohnolog genes according to their expression properties.…”

Section: Discussionmentioning

confidence: 99%

The structural variation landscape in 492 Atlantic salmon genomes

et al. 2020

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Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

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Section: Discussionmentioning

confidence: 99%

The structural variation landscape in 492 Atlantic salmon genomes

et al. 2020

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“…Previous studies have also evidenced the effect of TEs on deleteriousness in other salmonids. In common garden environments, hybrid breakdown in Lake whitefish ( Coregonus clupeaformis ) has been associated with TE reactivation caused by a genomic shock (genomic incompatibility) and associated hypomethylation in hybrids, leading to a malformed phenotype and aneuploidy (Dion‐Côté, Renaut, Normandeau, & Bernatchez, 2014; Dion‐Côté et al, 2017; Laporte et al., 2019). Overall, this highlights the importance of increasing our understanding of the (mal)adaptive role of such structural variants compared to SNP variation, especially in small populations (Mérot, Oomen, Tigano, & Wellenreuther, 2020).…”

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confidence: 99%

Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study

et al. 2020

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Investigating the relative importance of neutral versus selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (Salvelinus fontinalis) from Québec, Canada, as a case study, we investigated the importance of demographic versus selective processes governing the accumulation of both adaptive and maladaptive mutations in closed versus open and connected populations to assess gene flow effect. This was achieved by using 14,779 high‐quality filtered SNPs genotyped among 1,416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the PROVEAN algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation.

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“…SVs are increasingly recognized for their important role in a wide spectrum of evolutionary processes such as in environmental adaptation (Van't Hof et al, 2016;Wellenreuther, Rosenquist, Jakson, & Larson, 2017), reproductive isolation (Berdan, Blanckaert, Butlin, & Bank, 2019;Laporte et al, 2019), life cycles and development (Mérot et al, 2018;Cayuela et al, 2020) and speciation (Rieseberg, 2001; Serrato-Capuchina & Matute, 2018).…”

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Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species

et al. 2020

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DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species

Abstract: We present evidence for the dual role of epigenetics and transposable elements have a dual role in the reproductive isolation of nascent species.

Cited by 52 publications

References 48 publications

The structural variation landscape in 492 Atlantic salmon genomes

The structural variation landscape in 492 Atlantic salmon genomes

Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study

Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species

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