TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species...

Area of Science:

• Genomics
• Molecular Biology
• Population Genetics

Background:

• Transposable elements (TEs) are mobile genetic sequences that contribute significantly to genome evolution and genetic diversity.
• TEs play crucial roles in various biological processes, including immunity and adaptation during domestication.
• Analyzing TEs in non-model organisms and wild populations is challenging due to the lack of reference genomes or known TE loci.

Purpose of the Study:

• To develop a user-friendly and efficient computational tool, TEPEAK, for identifying and characterizing transposable elements (TEs) in populations.
• To enable TE analysis without requiring prior sequence or loci information, facilitating studies in under-researched species.
• To integrate with public databases like NCBI SRA for expanded cohort analysis.

Main Methods:

• TEPEAK was developed as a simple and efficient computational approach for TE identification and characterization.
• The tool processes user-submitted genomes and can integrate data from the NCBI Sequence Read Archive (SRA).
• TEPEAK was applied to analyze 257 horse genomes across 11 distinct groups.

Main Results:

• The application of TEPEAK to horse genomes successfully reaffirmed known genetic histories.
• Analysis revealed significant disruptions in crucial genes potentially mediated by TEs.
• Identified TEs in horses were also found in closely related species, suggesting conserved TE activity.

Conclusions:

• TEPEAK provides a simplified and powerful method for comprehensive genetic variation analysis, particularly for transposable elements in understudied populations.
• The tool enhances the study of genetic diversity and evolutionary dynamics by making TE analysis more accessible.
• TEPEAK is an open-source resource that will advance population genomics research.