Integrative genomics refines tissues, candidate genes and putative
regulatory links involved in the humic adaptation of keystone freshwater
fish
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.