Mobilomics in Saccharomyces cerevisiae strains

Area of Science:

• Genomics
• Computational Biology
• Molecular Evolution

Background:

• Mobile Genetic Elements (MGEs) are DNA sequences that can move within a genome.
• Current MGE detection relies on comparing sequences against known MGEs.
• Discovering all MGEs and their dynamics requires analyzing large comparative genomics datasets, necessitating computational efficiency.

Purpose of the Study:

• To develop a computational approach for discovering MGEs within genomes.
• To alleviate the computational burden associated with comparative genomics for MGE identification.
• To enable MGE discovery without requiring template sequences.

Main Methods:

• Utilized a progressive comparative genomics strategy exploiting high similarity between homologous chromosomes of closely related strains.
• Developed and applied a fast algorithm and software tool named regender to identify conserved regions between chromosomes.
• Analyzed non-conserved regions to identify MGEs, specifically Ty retrotransposons, and other putative mobile elements (PMEs).

Main Results:

• Regender efficiently compared 39 S. cerevisiae strains in minutes.
• Successfully located known Ty elements and mapped putative Tys across all strains.
• Identified PMEs as markers of inter-specific evolution and demonstrated their utility in inferring evolutionary relationships, similar to SNP-based phylogenies.

Conclusions:

• The proposed methodology effectively identifies MGEs without needing template sequences.
• Applicable to MGE inference in low-coverage genomes with unresolved bases, overcoming limitations of traditional methods.
• Offers a significant advancement for mobilomics and understanding genome dynamics.