DARTS: An Algorithm for Domain-Associated Retrotransposon Search in Genome Assemblies

Area of Science:

• Genomics
• Bioinformatics
• Molecular Evolution

Background:

• Retrotransposons are significant components of eukaryotic genomes, particularly in plants.
• Existing tools for transposable element (TE) mining often lack detailed lineage classification and protein domain analysis.
• Research into retrotransposon diversity and evolution necessitates adaptable computational methods.

Purpose of the Study:

• To develop a novel computational pipeline for identifying protein-coding retrotransposons using conserved protein domains.
• To improve the sensitivity and customizability of retrotransposon identification and annotation.
• To facilitate the study of retrotransposon evolution and diversity in plant genomes.

Main Methods:

• Development of the Domain-Associated Retrotransposon Search (DARTS) pipeline.
• Utilizing conserved protein domain sequences as a basis for mining retrotransposons.
• Comparative analysis of DARTS sensitivity against established tools like LTRharvest for long terminal repeat retrotransposons (LTR-RTs).

Main Results:

• DARTS demonstrates significantly higher sensitivity in identifying LTR-RTs compared to LTRharvest.
• The pipeline provides structurally annotated nucleotide and amino acid sequences.
• DARTS is customizable for specific research requirements.

Conclusions:

• DARTS offers a sensitive and adaptable approach for discovering and analyzing protein-coding retrotransposons.
• The tool facilitates comparative and phylogenetic analyses of retrotransposons, especially LTR-RTs in plants.
• DARTS is expected to advance research into the diversity and evolution of plant transposable elements.