Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Macqueen, Daniel J.; Primmer, Craig R.; Houston, Ross D.; Nowak, Barbara F.; Bernatchez, Louis; Bergseth, Steinar; Davidson, William S.; Gallardo‐Escárate, Cristian; Goldammer, Tom; Guiguen, Yann; Iturra, Patricia; Kijas, James W.; Koop, Ben F.; Lien, Sigbjørn; Maass, Alejandro; Martín, Samuel; McGinnity, Philip; Montecino, Martín; Naish, Kerry A.; Nichols, Krista M.; Olafsson, Kristinn; Omholt, Stig W.; Palti, Yniv; Plastow, Graham; Rexroad, Caird E.; Rise, Matthew L.; Ritchie, Rachael J.; Sandve, Simen Rød; Schulte, Patricia M.; Tello, Alfredo; Vidal, Rodrigo; Vik, Jon Olav; Wargelius, Anna; Yáñez, José M.

doi:10.1186/s12864-017-3862-8

Cited by 85 publications

(89 citation statements)

References 67 publications

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“…Future studies combining population genomic and quantitative genetic framework would then provide a more inclusive approach for uncovering the molecular footprints of domestication in Atlantic salmon. Furthermore, the complete functional annotation of the Atlantic salmon genome will undoubtedly enhance opportunities for a comprehensive understanding of the effects of domestication in Atlantic salmon populations (Macqueen et al, 2017).…”

Section: Limitations Of Genome Scan Methodsmentioning

confidence: 99%

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

López

Benestan

Moore

et al. 2018

Evolutionary Applications

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Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population‐specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.

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Section: Limitations Of Genome Scan Methodsmentioning

confidence: 99%

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

López

Benestan

Moore

et al. 2018

Evolutionary Applications

Self Cite

View full text Add to dashboard Cite

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“…The steady decrease in sequencing cost promised by new technologies suggests that access to the genome sequence may in the near future no longer be an unsurmountable obstacle for nonmodel species (Goodwin et al, 2016). Proof of this are the multiple international initiatives that are collaboratively sequencing genomes of various taxa including fungi (Grigoriev et al, 2014), invertebrates (GIGA 2014), arthropods (Evans et al, 2013), birds (Zhang, 2015), fishes (Macqueen et al, (2017); Malmstrøm, Matschiner, Tørresen, Jakobsen, & Jentoft, 2017), mammals (Fontanesi et al, 2016), vertebrates (Koepfli, Paten, & O'Brien, 2015), among others. genotype calling, as multiple reads (observations) help distinguish true variation from sequencing error (Nagasaki et al, 2015).…”

Section: Box 2 Continuedmentioning

confidence: 99%

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

2017

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Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.

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“…Gene annotation and accurate knowledge of the function of different identified regions is of extreme importance if genomic tools are to be used reliably in conservation and management (Ekblom & Wolf, ). Therefore, projects such as the ‘Functional Annotation of All Salmonid Genomes’ (Macqueen et al, ) should be encouraged and developed. It is also important not to underestimate or neglect the computing power and bioinformatics expertise required to produce high quality genome scaffolds and annotations, and also to recognise and account for biases in next generation sequencing data (Benestan et al, ).…”

Section: Molecular Toolsmentioning

confidence: 99%

Understanding and managing fish populations: keeping the toolbox fit for purpose

Paris

Sherman

Bell

et al. 2018

Journal of Fish Biology

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Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of The Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.

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Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Cited by 85 publications

References 67 publications

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Understanding and managing fish populations: keeping the toolbox fit for purpose

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