The structural variation landscape in 492 Atlantic salmon genomes

Area of Science:

• Genomics
• Evolutionary Biology
• Aquaculture

Background:

• Structural variants (SVs) are crucial for genetic diversity but are difficult to characterize in many species.
• Accurate SV typing is essential for understanding genome evolution and phenotypic variation.

Purpose of the Study:

• To develop a reliable method for structural variant discovery in non-model species.
• To characterize SVs in Atlantic salmon (Salmo salar L.) and investigate their role in evolution and domestication.

Main Methods:

• Whole genome sequencing of 492 Atlantic salmon individuals.
• Development and application of a novel approach for high-confidence SV discovery.
• Analysis of SV distribution, functional impact, and allele frequency changes.

Main Results:

• Identified 15,483 high-confidence SVs in Atlantic salmon.
• SVs accurately reflect population genetic structure and include an active DNA transposon.
• Discovered significant overlap between SVs and duplicated genes from an ancestral tetraploidization event.
• Observed changes in SV allele frequencies between wild and farmed salmon, indicating selection on behavioral traits.

Conclusions:

• The study provides a robust framework for SV discovery in non-model organisms.
• SVs play a significant role in Atlantic salmon genome evolution and the genetic basis of domestication traits.
• Domestication selection targets brain-expressed synaptic networks, with implications for human neurological disorders.