Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Temperate phages have a lysogenic cycle where they integrate into the host genome as prophages.
• Identifying highly divergent prophages is difficult using traditional methods based on gene similarity.

Purpose of the Study:

• To develop a novel computational tool, Prophage Tracer, for identifying active prophages in prokaryotic genomes.
• To enable the discovery of novel temperate phages and mobile genetic elements independent of sequence homology.

Main Methods:

• Prophage Tracer utilizes the lysis-lysogeny switch mechanism of temperate phages.
• It identifies prophage excision signals by detecting overlapping split-read alignments of bacterial (attB) and phage (attP) attachment sites.
• The tool analyzes short-read sequencing data.

Main Results:

• Prophage Tracer accurately predicted known prophages with precise boundaries.
• It successfully identified novel prophages, including dsDNA and ssDNA types in coral-associated bacteria, with highly divergent major capsid proteins.
• The tool demonstrated reliability in data mining for prophage discovery.

Conclusions:

• Prophage Tracer is an effective tool for identifying active prophages, including novel and divergent ones.
• It advances the study of temperate phages and mobile genetic elements in prokaryotic genomes.
• The tool facilitates the discovery of new phages and their biological roles.