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Integrative Genomics Refines Tissues, Candidate Genes and Putative Regulatory Links Involved in the Humic Adaptation
M Yu Ozerov1, K Noreikiene2,3, K Taube2
1Biodiversity Unit, University of Turku, Turku, Finland.
Molecular Ecology
|February 18, 2025
Summary
This study identifies key genes and tissues involved in the humic adaptation of Eurasian perch. By integrating genomic and transcriptomic data, researchers pinpointed specific molecular mechanisms driving adaptation in this freshwater fish.
Area of Science:
- Evolutionary genomics
- Functional genomics
- Freshwater fish adaptation
Background:
- Population genomics identifies selected genomic regions but struggles to link them to molecular mechanisms.
- Understanding the genetic basis of adaptation requires integrating evolutionary and functional data.
Purpose of the Study:
- To identify tissues, candidate genes, and SNP-gene expression associations involved in humic adaptation in Eurasian perch.
- To integrate population genomics and multi-tissue transcriptomics for a deeper understanding of adaptive processes.
Main Methods:
- Analyzed multi-tissue transcriptomes (gill, spleen, olfactory rosette, eye, liver) from 16 wild Eurasian perch populations.
- Integrated transcriptomic data with existing footprints of selection to prioritize candidate genes and adaptive variants.
- Identified differentially expressed genes (DEGs) and cis-expression quantitative trait loci (cis-eQTLs) to link genetic variation with gene expression.
Main Results:
- Over 5000 differentially expressed genes (DEGs) were identified across five tissues.
- Gill and spleen tissues showed a significant excess of outlier SNPs among DEGs, suggesting their role in humic adaptation.
- Significant enrichment of outlier expression-associated SNPs (eSNPs) was observed in spleen and olfactory rosette tissues, with several eQTLs located in regions of strong selection.
Conclusions:
- Specific organs like the gill and spleen play crucial roles in humic adaptation.
- The study prioritizes candidate genes under divergent selection by analyzing their expression patterns.
- This integrative approach provides a framework for understanding the genetic basis of phenotypic diversification and adaptation in diverse species.
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