First crAss-Like Phage Genome Encoding the Diversity-Generating Retroelement (DGR).

Area of Science:

• Virology
• Microbial Genomics
• Molecular Evolution

Background:

• The fecal virome harbors diverse bacteriophages, including crAss-like phages.
• Diversity-generating retroelements (DGRs) are mobile genetic elements that confer host specificity through hypermutation.

Purpose of the Study:

• To characterize a newly discovered crAss-like phage genome from a human fecal virome.
• To investigate the presence and architecture of DGRs in the AlphacrAssvirinae subfamily.

Main Methods:

• Metagenomic sequencing of fecal virome samples.
• Bioinformatic analysis of phage genomes and DGR-cassette components.
• Comparative genomics of crAss-like phage genomes.

Main Results:

• A novel crAss-like phage, crAssphage LMMB, was identified, belonging to candidate genus I of the AlphacrAssvirinae subfamily.
• crAssphage LMMB possesses a complete DGR cassette with the architecture TG-VR(IMH)-TR(IMH*)-RT, lacking an accessory variable determinant.
• Analysis of 91 related genomes revealed that 16% contained complete DGRs similar to crAssphage LMMB, while many others had incomplete DGRs.

Conclusions:

• The discovery of crAssphage LMMB expands our understanding of crAss-like phage diversity and DGR encoding.
• The conserved DGR architecture in a subset of genus I AlphacrAssvirinae suggests a functional role and potential horizontal gene transfer.