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Integrative genomics refines tissues, candidate genes and putative regulatory links involved in the humic adaptation of keystone freshwater fish
  • +2
  • Mikhail Ozerov,
  • Kristina Noreikiene,
  • Konrad Taube,
  • Riho Gross,
  • Anti Vasemägi
Mikhail Ozerov
University of Turku
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Kristina Noreikiene
Estonian University of Life Sciences
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Konrad Taube
Estonian University of Life Sciences
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Riho Gross
Estonian University of Life Sciences
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Anti Vasemägi
Swedish University of Agricultural Sciences Department of Aquatic Resources

Corresponding Author:[email protected]

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Abstract

Although population genomics approaches have been successful in identifying regions of the genome shaped by natural selection, the progress in dissecting the molecular mechanisms of adaptive variants and traits has been slow. By integrating multi-tissue (gill, spleen, olfactory rosette, whole eye and liver) transcriptomes from 16 wild Eurasian perch (Perca fluviatilis) populations and previously identified footprints of selection based on whole genome scan, we prioritize tissues, candidate genes and putative SNP-gene expression associations involved in humic adaptation of this keystone freshwater fish. Over 5,000 differentially expressed genes (DEGs) were discovered across the five tissues. A significant excess of outlier SNPs among DEGs found in the gill and spleen tissues indicated their involvement in humic adaptation. Further, 3,617 cis-eQTLs that associate with gene expression variation in perch were identified, with approximately 9% of genes harbouring cis-eQTLs showing differential expression between humic and clear-water habitats. Several cis-eQTLs were found in the regions showing most consistent signals of selection also harbouring DEGs (chr. 5: PLAGL2, chr. 7: PPP1R8, TCHH, chr. 8: IFITM3). Thus, our integrative analyses enabled to pinpoint specific organs that play a key role in adaptation, prioritize candidate genes under divergent selection based on their expression patterns, and identify links between SNPs and transcript abundance variation. We expect that the multi-omics strategy outlined in this work provides a practical framework for understanding the genetic basis of phenotypic diversification and adaptation for wide range of species.
Submitted to Molecular Ecology
Submission Checks Completed
Assigned to Editor
Reviewer(s) Assigned
08 Jul 2024Review(s) Completed, Editorial Evaluation Pending
16 Jul 2024Reviewer(s) Assigned
16 Sep 2024Editorial Decision: Revise Minor
30 Oct 20241st Revision Received
03 Nov 2024Submission Checks Completed
03 Nov 2024Assigned to Editor
03 Nov 2024Review(s) Completed, Editorial Evaluation Pending