Transposable element-mediated structural variation analysis in dog breeds using whole-genome sequencing.

Area of Science:

• Genomics
• Comparative genomics
• Canine genetics

Background:

• Naturally occurring canine diseases serve as models for human conditions like cancer and autoimmune disorders.
• Transposable elements (TEs) constitute approximately 31% of the dog genome and are key drivers of genomic variation and gene expression changes.
• Genomic variations induced by TEs can lead to genetic diseases in dogs.

Purpose of the Study:

• To detect and analyze structural variations (SVs) in the genomes of three dog breeds: Maltese, Poodle, and Yorkshire Terrier.
• To investigate the role of transposable elements in driving genomic variation and potential disease-related genetic changes within these breeds.
• To determine the recent activity and polymorphic nature of SVs, particularly those involving TEs, in the dog genome.

Main Methods:

• Whole-genome sequencing was performed on three distinct dog breeds.
• Structural variations (SVs) were identified and visualized using the BreakDancer program.
• Candidate SVs in genic regions were experimentally verified and their polymorphism analyzed via PCR assay.

Main Results:

• A total of 2328 deletion SV events were identified across the three breeds compared to the Boxer reference genome.
• Transposable element insertion polymorphism constituted the majority of detected variants (1229), followed by TE-mediated deletions (489) and non-TE-mediated deletions (542).
• Among TE insertions, 286 were full-length LINE-1s (L1s); 49 SV candidates in genic regions were verified and shown to be polymorphic within and between breeds, suggesting recent occurrence.

Conclusions:

• Transposable elements significantly contribute to genomic variation among the Maltese, Poodle, and Yorkshire Terrier breeds.
• The polymorphic nature of identified SVs indicates recent retrotransposition events within the dog genome.
• Understanding TE-mediated genomic variations is crucial for studying canine genetic diseases and their relevance as models for human disorders.