Phagengenom

PhagenGenom, or the phagenome, is the collective genetic material of bacteriophages, the viruses that infect bacteria. It covers the diverse genome types and organizations found across phage lineages, including double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and some RNA phages. Phagenomes vary widely in size, from about 5 kilobases in some ssDNA phages to over 200 kilobases in large dsDNA phages. Phagenomic studies address viral evolution, ecology, and the roles phages play in microbial communities. Phages can be lytic or lysogenic, and many phage genomes are mosaics of modular gene blocks.

Genome organization in phagenomes is typically modular, with blocks for replication and regulation, structural and assembly proteins, and lysis or lysogeny functions. Some genomes carry auxiliary metabolic genes that influence host metabolism during infection. The architecture is often mosaic, reflecting frequent horizontal gene transfer and recombination among phages and their bacterial hosts.

Advances in sequencing have accelerated phagenomics, enabling rapid assembly and annotation of complete genomes. Annotation identifies open reading frames, tRNA genes, regulatory elements, and noncoding RNAs, though many phage genes have unknown functions. Public databases such as GenBank and RefSeq organize phage genomes, support taxonomy, and enable comparative analyses and outbreak tracking.

PhagenGenom studies inform phage therapy, biotechnology, and ecology, revealing phage-host interactions, viral evolution, and the impact of phages on ecosystems. Ongoing challenges include the high genetic diversity of phages, rapid evolution, and a large fraction of novel genes without known function, which complicates annotation and risk assessment.