crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes

Abstract

crAssphages are a broad group of diverse bacteriophages in the order Caudovirales that have been found to be highly abundant in the human gastrointestinal tract. Despite their high prevalence, we have an incomplete understanding of how crAssphages shape and respond to ecological and evolutionary dynamics in the gut. Here, we report genomes of crAssphages from feces of one South African woman and three infants. Across the complete genome sequences of the South African crAssphages described here, we identify particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, contrasted against purifying selection, genome-wide. We further validate these findings against a crAssphage genome from previous studies. Together, our results suggest hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.

Keywords: Bacteriophage; Selection; South Africa; Tail protein; crAssphage.

Figure 1.. Summary of crAssphage genomes identified in this study (in bold) as well as those that are most closely related.

A. Details of the read coverage and mapping for the five South African crAssphages identified in study and a pairwise identity comparison of the most closely related crAssphage genomes. B. An unrooted Maximum Likelihood phylogenetic tree inferred using PHYML 3.0 (Criscuolo, 2011) with substitution model GTR+G+I. Bootstrapped (1000 iterations) branch support is provided at each branch. C. Illustration of the crAssphages genome organization. Genes /coding regions discusses further in the manuscript are color codes. Blastn based similarity between genomes was determined using EasyFig (Sullivan et al., 2011) are shown.

Figure 2.. Selective pressures are variable across the genome of several South African crAssphages.

A. The distribution of variants per kilobase across the genomes of three South African crAssphages. The region encoding RNA polymerase genes is colored blue. The region encoding phage tail proteins is colored red. B. The fold coverage of quality filtered reads across the genomes of each crAssphage taxon. CrAssphages M186D4 (MK238400) in grey lines, C0521BW15 (MW067001) in orange lines, C0526BW15 (MW067002) in blue lines.