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Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing.

Sixin Liu1, Guangtu Gao1, Ryan M Layer2,3

  • 1National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States.

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|March 18, 2021
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Summary

This study identified 13,863 structural variants (SVs) in rainbow trout using whole-genome sequencing. Transposable elements significantly contribute to these SVs, offering insights into genetic variation in this aquaculture species.

Keywords:
copy number variantsrainbow troutrepetitive sequencestructural variantstransposable elementswhole-genome sequencing

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Area of Science:

  • Genomics
  • Aquaculture Science

Background:

  • Genomic structural variants (SVs) are key drivers of genetic and phenotypic diversity.
  • Systematic investigation of SVs in rainbow trout (Oncorhynchus mykiss), a vital freshwater aquaculture species, is lacking.

Purpose of the Study:

  • To identify and validate high-confidence SVs in rainbow trout.
  • To assess the role of transposable elements (TEs) in generating SVs within the rainbow trout genome.

Main Methods:

  • Whole-genome re-sequencing of 96 rainbow trout (11 homozygous lines, 85 outbred fish).
  • Identification of SVs using the Smoove program, followed by rigorous filtering.
  • Validation of SVs using Pacific Biosciences long-read sequencing.

Main Results:

  • 13,863 high-confidence SVs were identified and validated with 98% accuracy.
  • Outbred fish grouped by population, confirming SV robustness.
  • SV sequences showed significantly higher repetitive DNA content (86.5%) compared to the reference genome (57.1%), indicating substantial TE contribution.

Conclusions:

  • Transposable elements are major contributors to structural variants in rainbow trout.
  • Identified SVs, including exon-loss and gene-fusion variants, may influence phenotypes.
  • This comprehensive SV dataset provides a foundation for future research in rainbow trout genomics and breeding.