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.
Fig: Overview of the different steps involved in the PhageTermVirome workflow. Virome sequencing reads are simultaneously mapped to numerous contigs assembled from the virome dataset. After alignments for each contig, PTV performs peak detection and statistical analyses to determine the position of significant termini. On all contigs for which termini were detected, a coverage pattern analysis is achieved to predict the corresponding genome packaging mechanism. aThe sequencing method and library preparation require the preservation of genome ends (ex: all methods involving random DNA fragmentation prior to library preparation and long-read sequencing of intact DNA). bPhageTermVirome can process massive amount of contigs as input (multifasta), but still allow users to analyze a single phage contig (fasta).
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.
Garneau, J.R., Legrand, V., Marbouty, M. et al. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. Sci Rep 11, 18319 (2021). https://doi.org/10.1038/s41598-021-97867-3