Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species

TL;DR

Arctic codfish species show rapid genome changes like chromosomal fusions and inversions, which may help them adapt to freezing environments.

Contribution

The study reveals lineage-specific chromosomal fusions and TE-driven inversions in Arctic codfish genomes, linking them to adaptation.

Findings

Arctic cod has eight chromosomal fusions, polar cod has five, linked to their geographic distribution.

Chromosomal inversions in Arctic cod are enriched with specific transposable element families.

MITEs are involved in expanding antifreeze glycoprotein genes in polar cod.

Abstract

Genome evolvability involves activation of transposable elements (TEs) that result in novel genomic rearrangements, including translocations, deletions, duplications, as well as larger structural reorganizations, such as chromosomal inversions and fusions. These genomic modifications contribute to raw genetic variability in which selection can act upon, and thus, promote local adaptation.

Using a comparative genomics framework combined with the generation of six chromosome-level gadid reference genomes, including the cold-water adapted polar cod (Boreogadus saida) and Arctic cod (Arctogadus glacialis), we uncover an array of larger and smaller chromosomal reorganizations within this lineage. For the two Arctic codfishes, we detect lineage-specific chromosomal fusions, i.e., five in polar cod vs. eight in Arctic cod, resulting in a reduced number of chromosomes found to be associated with their geographical distribution. For the same species, we identify a high number of partly overlapping chromosomal inversions where a majority (especially within breakpoint regions) display an overrepresentation of specific TE families, accompanied by signatures of high degree of conservation. We further demonstrate involvement of miniature inverted-repeat transposable elements (MITEs) in the expansion of the well-known antifreeze glycoprotein genes in polar cod, and that the three gene clusters were localized in association with chromosomal rearrangements on chromosomes 1, 2, and 14.

We characterize how the Gadidae lineage has undergone massive genomic modifications — potentially via activation of TEs — throughout their evolutionary history, and particularly for the more Arctic species. These genomic reorganizations have likely played an important role in divergence processes and adaptation to freezing environmental conditions.

The online version contains supplementary material available at 10.1186/s13059-026-03975-6.

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