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Research article
Eeva Jansson
Havforskningsinstituttet
Corresponding Author
ORCiD: https://orcid.org/0000-0002-7840-7201
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies.
Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence (FST>0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly (p<0.05) differentiated (mean FST_173_loci=0.065, FST_69_loci=0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin.
Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
Keywords
assignment, Ctenolabrus rupestris, marker validation, population genomics, resequencing, SNP
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View the published article at BMC Genomic Data.
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Posted 21 Sep, 2020
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Editorial decision: Accept
On 21 Sep, 2020
Editor assigned
On 17 Sep, 2020
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On 16 Sep, 2020
Editor invited
On 16 Sep, 2020
No comments provided
Editorial decision: Minor revision
On 05 Jun, 2020
Review #2 received
Received 31 Mar, 2020
Review #1 received
Received 26 Mar, 2020
Reviewer #2 agreed
On 07 Mar, 2020
Reviewer #1 agreed
On 05 Mar, 2020
Reviewers invited
Invitations sent on 05 Feb, 2020
Editor assigned
On 03 Feb, 2020
Submission checks complete
On 28 Jan, 2020
Editor invited
On 27 Jan, 2020
First submitted
On 21 Jan, 2020
Version (no preprint)
Posted 30 Jan, 2020
Editorial decision: Minor revision
On 04 Sep, 2020
Review #2 received
Received 02 Sep, 2020
Review #1 received
Received 02 Aug, 2020
Reviewer #2 agreed
On 13 Jul, 2020
Reviewer #1 agreed
On 10 Jul, 2020
Editor assigned
On 09 Jul, 2020
Reviewers invited
Invitations sent on 09 Jul, 2020
Submission checks complete
On 08 Jul, 2020
Editor invited
On 08 Jul, 2020
This version was not preprinted
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Population Genetics
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See the published version of this preprint at BMC Genomic Data.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Eeva Jansson
Havforskningsinstituttet
Corresponding Author
ORCiD: https://orcid.org/0000-0002-7840-7201
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomic Data.
Version 2
Posted 21 Sep, 2020
No community comments so far
Editorial decision: Accept
On 21 Sep, 2020
Editor assigned
On 17 Sep, 2020
Submission checks complete
On 16 Sep, 2020
Editor invited
On 16 Sep, 2020
No comments provided
Editorial decision: Minor revision
On 05 Jun, 2020
Review #2 received
Received 31 Mar, 2020
Review #1 received
Received 26 Mar, 2020
Reviewer #2 agreed
On 07 Mar, 2020
Reviewer #1 agreed
On 05 Mar, 2020
Reviewers invited
Invitations sent on 05 Feb, 2020
Editor assigned
On 03 Feb, 2020
Submission checks complete
On 28 Jan, 2020
Editor invited
On 27 Jan, 2020
First submitted
On 21 Jan, 2020
Version (no preprint)
Posted 30 Jan, 2020
Editorial decision: Minor revision
On 04 Sep, 2020
Review #2 received
Received 02 Sep, 2020
Review #1 received
Received 02 Aug, 2020
Reviewer #2 agreed
On 13 Jul, 2020
Reviewer #1 agreed
On 10 Jul, 2020
Editor assigned
On 09 Jul, 2020
Reviewers invited
Invitations sent on 09 Jul, 2020
Submission checks complete
On 08 Jul, 2020
Editor invited
On 08 Jul, 2020
This version was not preprinted
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Population Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomic Data.
Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies.
Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence (FST>0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly (p<0.05) differentiated (mean FST_173_loci=0.065, FST_69_loci=0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin.
Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
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