High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome

Julian R Garneau,Véronique Legrand,Matthew B Sullivan,Martial Marbouty,David Bikard,Dean R Vik,Maximilian O Press,Louis-Charles Fortier,Marc Monot

doi:10.1038/s41598-021-97867-3

Abstract

Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv.

Highlights

Viruses that infect bacteria are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging
It has been previously shown that the ends of linear DNA, a hallmark of genomic DNA packaged in the capsid of free phage particles, can be detected from shotgun sequencing data if the sequencing library was prepared in a way that preserves such DNA ends[26,27]
DNA fragments with one end that corresponds to natural genome termini will be strongly enriched relative to other DNA fragments that end at random positions due to the random fragmentation of DNA during library preparation

Summary

Introduction

Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. We introduce PhageTermVirome (PTV), an easy-to-use bioinformatics software that efficiently identifies critical information such as phage genome termini and packaging mechanisms in modern large-scale viral metagenomics datasets.

Results

Conclusion