Efficient detection and typing of phage-plasmids

TL;DR

This paper introduces tyPPing, a new method to accurately detect and classify phage-plasmids, which are hybrid genetic elements that are often misclassified by existing tools.

Contribution

The paper introduces tyPPing, a novel computational method for precise and systematic detection and typing of phage-plasmids.

Findings

tyPPing accurately separates phage-plasmids from phages and plasmids using conserved protein frequencies.

tyPPing outperforms existing tools in sensitivity and scalability for phage-plasmid classification.

tyPPing was validated on diverse datasets and experimentally confirmed to identify functional phage-plasmids.

Abstract

Phage-plasmids (P-Ps) are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges and to the formation of hybrid or defective elements, which limits accurate detection of P-Ps. To address this challenge, we developed tyPPing, an easy-to-use method that efficiently detects and types P-Ps with high accuracy. It searches for distinct frequencies and sets of conserved proteins to separate P-Ps from plasmids and phages. tyPPing’s strength comes from both its precise predictions and its ability to systematically type P-Ps, including the assignment of confidence levels. We tested tyPPing on several databases and a collection of incomplete (draft) genomes. While predictions rely on the quality of assemblies, we detected high-quality P-Ps and experimentally proved them to be functional. Compared to other classification methods, tyPPing is designed to detect distinct P-P types and surpasses other tools in terms of sensitivity and scalability. P-Ps are highly diverse, making the systematic identification of new types a difficult task. By combining tyPPing with other tools, however, we show a valuable foundation for addressing this challenge. How to use tyPPing and other approaches is documented in our GitHub repository: github.com/EpfeiferNutri/Phage-plasmids/.

Mobile genetic elements, such as phages and plasmids, are diverse and drive bacterial evolution through horizontal gene transfer. Phage-plasmids, of which many carry antibiotic resistance genes or virulence factors, are both phages and plasmids and have life cycles of temperate phages and plasmids. This makes accurate classification difficult as current computational tools typically classify them as one or the other. We addressed this problem by developing tyPPing, a new and highly precise method, to systematically identify, separate, and catalog phage-plasmids. We demonstrated that tyPPing is highly accurate and broadly compatible. It provides a reliable foundation for all future studies involving phages and plasmids, ranging from agriculture environments to pathogenic strains of clinical settings.

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