The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

TLDR

Whole‑genome duplications have shaped vertebrate evolution, linking rare duplication events to adaptive radiations and evolutionary innovations. The study aims to use the rainbow trout genome to investigate the early evolutionary fate of a duplicated vertebrate genome following an additional round of WGD. The authors sequenced the rainbow trout genome to analyze rediploidization patterns after WGD. After 100 million years, the two ancestral subgenomes remain highly collinear despite losing half of duplicated protein‑coding genes through pseudogenization, while most miRNA genes are retained as duplicates, revealing a slow, stepwise rediploidization that contradicts the hypothesis of rapid genomic reorganization.

Abstract

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions. Although whole-genome duplications (WGDs) are rare events, they have an important role in shaping vertebrate evolution. Here, the authors sequence the rainbow trout genome and show that rediploidization after WGD occurs in a slow and stepwise manner.