Abstract
A new crAss-like genome encoding diversity-generating retroelement (DGR) was found in the fecal virome of a healthy volunteer. The genome of the phage referred to as the crAssphage LMMB, belonged to the candidate genus I of the AlphacrAssvirinae subfamily. The DGR-cassette of the crAssphage LMMB contained all the essential elements: the gene encoding reverse transcriptase (RT), the target gene (TG) encoding the tail-collar fiber protein, and variable and template repeats (VR and TR) with IMH (initiation of mutagenic homing) and IMH* sequences at the 3′-end of the VR and TR, respectively. Architecture of the DGR-cassette was TG-VR(IMH)-TR(IMH*)-RT and an accessory variable determinant (avd) was absent from the cassette. Analysis of 91 genomes and genome fragments from genus I of the AlphacrAssvirinae showed that 15 (16%) of the genomes had DGRs with the same architecture as the crAssphage LMMB, while 66 of the genomes contained incomplete DGR-cassettes or some elements of the DGR.
Highlights
CrAss-like phages have been discovered by computational analysis of human fecal metagenome data and their genomes have been shown to be the most abundant group of sequences in the human gut virome [1]
The sequence similarity analysis performed using the CGView server revealed that the studied genome of a phage, referred to as the crAssphage LMMB, showed gene synteny typical of other crAss-like genomes (Figure 1) from the candidate genus I of the previously suggested subfamily AlphacrAssvirinae, which contains p-crAssphage [3]
We describe the first finding of a diversity-generating retroelement (DGR)-cassette in the genome of the crAss-like phage
Summary
CrAss-like phages have been discovered by computational analysis of human fecal metagenome data and their genomes have been shown to be the most abundant group of sequences (up to 90%) in the human gut virome [1]. Intensive studies on the biology, taxonomy, and role of crAss-like phages have shown that they have high levels of genetic diversity. Members of this group of phages have been found in a range of environments, including the human gut and feces, termite gut, terrestrial/groundwater environments, soda lakes (hypersaline brine), marine sediments, and plant roots [2,3,5,6,7]. CrAss-like phages likely infect a variety of bacterial hosts; the mechanisms generating this variability are unknown
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