Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data

Area of Science:

• Genomics
• Evolutionary Biology
• Comparative Genomics

Background:

• Structural variation significantly impacts canine evolution and phenotypic diversity.
• Previous studies primarily used short-read sequencing, limiting the comprehensive assessment of structural variants.
• Advances in long-read sequencing offer improved detection of complex structural variations.

Purpose of the Study:

• To conduct an integrative analysis of structural variants in canines using both long-read and short-read sequencing data.
• To discover heterozygous variations and insertion variants missed by short-read approaches.
• To create a comprehensive catalog of structural variants in dogs and wolves.

Main Methods:

• Integrative analysis of structural variants in 12 canine samples with long-read and short-read sequencing data.
• Utilized long-reads for discovering heterozygous variation and insertion variants.
• Employed a graph-based approach to genotype structural variants in 1,879 dogs and wolves.

Main Results:

• Identified dimorphic LINE-1 and SINE variants comprising over 45% of all deletions.
• Discovered 1,410 LINE-1s with intact open reading frames showing presence-absence dimorphism.
• Generated a variant catalog with a 56.5% increase in deletions and a 705% increase in insertions.
• Identified 283 structural variants with signatures of selection across breed clades.

Conclusions:

• Long-read sequencing significantly enhances the discovery of structural variants, particularly insertions, in the canine genome.
• The expanded variant catalog provides a more complete understanding of canine genetic diversity and evolution.
• Identification of selected structural variants offers insights into breed-specific adaptations and phenotypic differences.