How does sequence variability affect<i>de novo</i>assembly quality?

Skern‐Mauritzen, Rasmus; Malde, Ketil; Besnier, François; Nilsen, Frank; Jonassen, Inge; Reinhardt, Richard; Koop, Ben F.; Dalvin, Sussie; Mæhle, Stig; Kongshaug, Heidi; Glover, Kevin A.

doi:10.1080/00222933.2012.738833

Cited by 5 publications

(6 citation statements)

References 14 publications

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“…In fact, Vasemagi et al (2012), observed non-significant differences in the levels of diversity between wild and domesticated strains, and one comparison showed higher diversity in the domesticated strain compared to its wild progenitor. The disproportionate loss of alleles in highly polymorphic as opposed to bi-allelic makers such as SNPs is expected and has been well documented in other organisms taken into culture, and even under strong inbreeding regimes (Hamre, Glover, & Nilsen, 2009;Skern-Mauritzen et al, 2013).…”

Section: Studies Of Molecular-genetic Markersmentioning

confidence: 94%

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

et al. 2017

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Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population-specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long-term consequences of introgression is expected to lead to changes in life-history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts. K E Y W O R D Saquaculture, evolution, fish farming, fitness, genetic, hybrid

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Section: Studies Of Molecular-genetic Markersmentioning

confidence: 94%

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

et al. 2017

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“…The fifth sample was collected in September 2008 from an emamectin-benzoate-desensitized population in Austevoll, Western Norway. Eight adult female L. salmonis were sampled from each of the five regions [ 75 ]. For all samples, DNA was isolated in a 96-well format using the DNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).…”

Section: Methodsmentioning

confidence: 99%

“…For all samples, DNA was isolated in a 96-well format using the DNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). Equal amounts of DNA from each of the eight individuals from each station were pooled to meet concentration demands and were sequenced by Fasteris SA using the Illumina HiSeq 2000 platform following their standard protocols [ 75 ]. In addition to the five regional samples, DNA was also sequenced from Expressed Sequence Tags (EST).…”

Section: Methodsmentioning

confidence: 99%

Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis

et al. 2014

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BackgroundThe salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. Lice control on farms is reliant upon a few groups of pesticides that have all shown time-limited efficiency due to resistance development. However, to date, this example of human-induced evolution is poorly documented at the population level due to the lack of molecular tools. As such, important evolutionary and management questions, linked to the development and dispersal of pesticide resistance in this parasite, remain unanswered. Here, we introduce the first Single Nucleotide Polymorphism (SNP) array for the salmon louse, which includes 6000 markers, and present a population genomic scan using this array on 576 lice from twelve farms distributed across the North Atlantic.ResultsOur results support the hypothesis of a single panmictic population of lice in the Atlantic, and importantly, revealed very strong selective sweeps on linkage groups 1 and 5. These sweeps included candidate genes potentially connected to pesticide resistance. After genotyping a further 576 lice from 12 full sibling families, a genome-wide association analysis established a highly significant association between the major sweep on linkage group 5 and resistance to emamectin benzoate, the most widely used pesticide in salmonid aquaculture for more than a decade.ConclusionsThe analysis of conserved haplotypes across samples from the Atlantic strongly suggests that emamectin benzoate resistance developed at a single source, and rapidly spread across the Atlantic within the period 1999 when the chemical was first introduced, to 2010 when samples for the present study were obtained. These results provide unique insights into the development and spread of pesticide resistance in the marine environment, and identify a small genomic region strongly linked to emamectin benzoate resistance. Finally, these results have highly significant implications for the way pesticide resistance is considered and managed within the aquaculture industry.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-937) contains supplementary material, which is available to authorized users.

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“…Data for this marker were acquired in the present study by genotyping all of the samples with this marker as described below; (ii) sequences for the mitochondrial genes A6 and Cyt b that were used to study spatial and temporal changes in mtDNA variation between the historical (Tjensvoll et al, 2006 ) and contemporary salmon lice samples; and (iii) genotypes at 15 microsatellite DNA loci. Microsatellites are highly effective in picking up strong demographic events such as inbreeding and strong population bottlenecks (Skaala et al, 2004 ; Skern‐Mauritzen et al, 2013 ). Microsatellites were therefore included in the present study to provide a presumed selectively neutral nDNA control for potential temporal or spatial patterns observed in the mtDNA variation.…”

Section: Methodsmentioning

confidence: 99%

“…(iii) genotypes at 15 microsatellite DNA loci. Microsatellites are highly effective in picking up strong demographic events such as inbreeding and strong population bottlenecks (Skaala et al, 2004;Skern-Mauritzen et al, 2013). Microsatellites were therefore included in the present study to provide a presumed selectively neutral nDNA control for potential temporal or spatial patterns observed in the mtDNA variation.…”

Section: Ta B L Ementioning

confidence: 99%

Aquaculture‐driven evolution of the salmon louse mtDNA genome

Rutle,

Skern‐Mauritzen,

Nilsen

et al. 2023

Evolutionary Applications

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Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000–2002 “pre‐resistance”) and contemporary (2014–2017 “post‐resistance”) samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as “neutral” controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000–2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long‐distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species.

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How does sequence variability affectde novoassembly quality?

Cited by 5 publications

References 14 publications

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis

Aquaculture‐driven evolution of the salmon louse mtDNA genome

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