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Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
Stockholm University, Faculty of Science, Department of Zoology.
Stockholm University, Faculty of Science, Department of Zoology.
Stockholm University, Faculty of Science, Department of Zoology.
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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Number of Authors: 102019 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, p. 11448-11463Article in journal (Refereed) Published
Abstract [en]

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

Place, publisher, year, edition, pages
2019. Vol. 9, p. 11448-11463
Keywords [en]
genetic diversity, genome sequencing, population genomics, Salmo trutta, salmonid, single nucleotide polymorphism
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-175045DOI: 10.1002/ece3.5646ISI: 000487783000001OAI: oai:DiVA.org:su-175045DiVA, id: diva2:1366447
Available from: 2019-10-29 Created: 2019-10-29 Last updated: 2019-12-12Bibliographically approved

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Kurland, SaraWheat, Christopher W.Celorio Mancera, Maria de la PazKutschera, Verena E.Hill, JasonAndersson, AnastasiaRyman, NilsLaikre, Linda
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Department of ZoologyScience for Life Laboratory (SciLifeLab)Department of Biochemistry and Biophysics
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