Evolutionary Study of the Crassphage Virus at Gene Level

Abstract

crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.

Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?

“…Gene duplication is one such strategy found in crAss-like sequences that is speculated to bestow replicative advantages. For instance, p-crAssphage has two copies of repL , required for the initiation of DNA replication, which arose from an ancient gene duplication event [ 43 ]. CrAss-like phages assigned to candidate genus I ( Crudevirinae subfamily of Intestiviridae ) have been found to encode diversity-generating retroelements associated with tail protein genes (DGR) [ 44 ].…”

Perspective on taxonomic classification of uncultivated viruses

“…For viruses with larger genomes such as tailed bacterial and archaeal viruses (class Caudoviricetes), concatenated protein phylogenies become practical [46 ]. Critically, the phylogenies of individual marker genes should be compared to a phylogeny based on a concatenated alignment to assess potential horizontal gene transfer and taxonomic biases [74][75][76].…”

Host interactions of novelCrassviralesspecies belonging to multiple families infecting bacterial host,Bacteroides cellulosilyticusWH2

“…The human gut microbiome has high bacterial densities, including a high abundance of Bacteroidota (formerly Bacteroidetes) (13)(14)(15), which are shaped by the phages that infect and kill them such as crAssphages. The dsDNA crAssphages have a podovirus-like morphology, genomes ranging between 100 and 200 kb, and conserved gene order (16)(17)(18). These bacteriophages are ubiquitous, can stably colonize an individual, and do not appear to be associated with health or disease states (17,19).…”