MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies

Area of Science:

• Genomics
• Bioinformatics
• Molecular Evolution

Background:

• Eukaryotic genomes contain numerous mobile genetic elements (MGEs), including transposons and retrotransposons, which significantly influence genome plasticity and evolution.
• Existing computational tools for MGE annotation often require de novo or homology-based approaches on genomic assemblies or raw reads.
• A gap exists in pipelines that provide readily usable coding and flanking sequences of MGEs from genome assemblies for downstream biological analysis.

Purpose of the Study:

• To develop an automated pipeline for retrieving mobile genetic elements (MGEs) and their associated sequences from genomic assemblies.
• To facilitate downstream biological analysis of MGEs by providing standardized coding and flanking sequences.

Main Methods:

• Development of a novel computational pipeline named MGERT (Mobile Genetic Elements Retrieving Tool).
• Automation of all necessary steps for extracting MGE protein-coding and flanking sequences from genomic assemblies.
• The pipeline functions effectively even when prior information on the MGE content of a genome is unavailable.

Main Results:

• Successful development of the MGERT pipeline, automating the retrieval of MGE sequences.
• MGERT enables the extraction of protein-coding sequences of MGEs from genomic assemblies.
• The tool provides flanking sequences essential for further analysis.

Conclusions:

• MGERT empowers researchers to efficiently identify MGEs and their coding/flanking sequences within any genome of interest.
• This pipeline significantly reduces the need for manual scripting and complex pipelining, allowing researchers to concentrate on the biological interpretation of MGEs.
• MGERT enhances the accessibility of MGE analysis in genomics research.