Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 5, 2025

Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model

Language: Английский

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Extinction risks and threats facing the freshwater fishes of Britain

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2023, Volume and Issue: 33(12), P. 1460 - 1476

Published: Sept. 19, 2023

Abstract Extinctions occur naturally in all environments, but rates have accelerated rapidly during the Anthropocene, especially fresh water. Despite supporting many fish species of conservation importance, there has never been a formal assessment their extinction risks Britain, which impeded inclusion relevant legislation and policy. This study therefore used International Union for Conservation Nature (IUCN) Red List Threatened Species™ Categories Criteria to conduct first systematic threats facing native freshwater diadromous fishes Britain. In addition, national assessments were produced England, Scotland Wales, reflecting level at environmental policy decisions are taken Seven categorized as being threatened with regional level, European eel Anguilla anguilla allis shad Alosa alosa classified Critically Endangered, Atlantic salmon Salmo salar , vendace Coregonus albula whitefish lavaretus Arctic charr Salvelinus alpinus twaite fallax Vulnerable. burbot Lota lota was Regionally Extinct, ferox trout Data Deficient, 25 Least Concern. sturgeon Acipenser sturio houting oxyrinchus although probably native, qualified only vagrants water, so Not Applicable. The provide objective baselines against future changes can be determined, key evidence base support management habitats It is recommended that repeated every 10 years, would enable status, effectiveness policies where targeted interventions may required examined using Index.

Language: Английский

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The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme

BMC Genomic Data, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 25, 2025

Abstract Objectives European whitefish ( Coregonus lavaretus L .) is a freshwater salmonid that inhabits cold regions of central and north Europe Siberia. It an important aquaculture species in Finland, selectively bred since 1999. The breeding programme has applied genomic selection uses SNP markers phenotypic data to improve traits such as growth, product quality, fish health. Salmonids are known for chromosomal rearrangements, the current C. reference genome based on individual from Switzerland may deviate Finnish one. Therefore, we have assembled whitefish. This allows us better assess genetic basis enhance accuracy selection. Data description was sequenced using combination Illumina PacBio technologies wtbg2 HiRise software. assembly size 2.94 Gb comprises 6,706 scaffolds with scaffold N50 1.36 Mb.

Language: Английский

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Rapid adaptation through genomic and epigenomic responses following translocations in an endangered salmonid

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(10), P. 2470 - 2489

Published: June 11, 2021

Identifying the molecular mechanisms facilitating adaptation to new environments is a key question in evolutionary biology, especially face of current rapid and human-induced changes. Translocations have become an important tool for species conservation, but attendant small population sizes ecological pressures might affect phenotypic genotypic variation trajectories dramatically unknown ways. In Scotland, European whitefish (

Language: Английский

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How glaciation impacted evolutionary history and contemporary genetic diversity of flora and fauna in the British Isles

Scottish Geographical Journal, Journal Year: 2023, Volume and Issue: 139(3-4), P. 445 - 465

Published: July 18, 2023

Ice coverage not only affects the climate and landscape of geographical regions but has impacted species composition, fragmentation isolation populations, colonisation routes post-glaciation. Major advancements in generating genetic data applying sophisticated analyses to accurately model demographic history animal plant allowed evolutionary biologists novel insights. Meanwhile, physical geographers have made major reconstructing glacial history. However, information flow between geographic fields on this topic remains limited; consequently, studies contemporary biodiversity tend be vague about role history, while is rarely leveraged when discussing historical glaciation. In review, we bring together current knowledge changing patterns ice British Isles from maximum extent British-Irish sheet (BIIS) ca. 27 ka through end large-scale at start Holocene period 11.5 ka. We do so then highlight how glaciation affected composition during time subsequent temperate flora fauna variation seen them.

Language: Английский

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How diverse is the toolbox? A review of management actions to conserve or restore coregonines

International Journal of Limnology, Journal Year: 2024, Volume and Issue: 60, P. 5 - 5

Published: Jan. 1, 2024

Over the past centuries, coregonines have been exposed to a range of stressors that led extinctions, extirpations, and speciation reversals. Given some populations remain at risk fishery managers begun restoring where they extirpated, we reviewed primary gray literature describe diversity coregonine restoration or conservation actions previously used. Although stocking hatchery-reared fish has commonly used for supplementing existing fisheries, considered efforts only with specifically goals. Likewise, conservation-driven translocation were not widespread, except in United Kingdom creation refuge supplement distribution declining stocks. Habitat occurred more broadly included improving spawning habitat, connectivity, nutrient concentrations. harvest regulations are regulate found fewer examples protected areas outright closures. Finally, interactions invasive species can be considerable stressor, yet relatively few control undertaken direct benefit coregonines. In conclusion, our review prior Coregonid symposia revealed limited emphasis on relative traditional approaches ( e.g. , supplementation stock assessment) studying life history genetics. Ideally, by providing this broad strategies, future management will from learning about greater potential could locally applied.

Language: Английский

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Testing the radiation cascade in postglacial radiations of whitefish and their parasites: founder events and host ecology drive parasite evolution

Evolution Letters, Journal Year: 2024, Volume and Issue: 8(5), P. 706 - 718

Published: June 19, 2024

Reciprocal effects of adaptive radiations on the evolution interspecific interactions, like parasitism, remain barely explored. We test whether recent European whitefish (

Language: Английский

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Complex and divergent histories gave rise to genome‐wide divergence patterns amongst European whitefish (Coregonus lavaretus)

Journal of Evolutionary Biology, Journal Year: 2021, Volume and Issue: 34(12), P. 1954 - 1969

Published: Oct. 17, 2021

Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion contemporary biodiversity complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish on mainland Europe, but Britain it has only seven native populations, all of which are found the western extremes island. origins colonization routes into unknown likely contributed to genetic patterns regional uniqueness. Here, we used up 25,751 genome-wide polymorphic loci reconstruct history discern demographic evolutionary forces underpinning divergence between British populations. Overall, lower diversity Scottish populations high differentiation (FST = 0.433-0.712) from English/Welsh other Differentiation was elevated rather than particular genomic regions. Demographic modelling supported Scotland northern refugia separate route for southern refugia, with these two groups having been separated more ca. 50 Ky. We cyto-nuclear discordance at scale, clustering closely Baltic population mtDNA analysis not nuclear data, Norwegian Alpine displaying same haplotype being distantly related tree. These findings suggest neutral processes, primarily drift regionally distinct pre-glacial histories, important drivers whitefish. This sheds new light establishment freshwater fauna after last glacial maximum.

Language: Английский

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Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 4, 2023

Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model

Language: Английский

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Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model

Language: Английский

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