From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are

During October I have been taking on an art challenge to develop drawing skills and habits through undertaking an ink drawing every day in October, based on a prompt word. After posting some microb…

Kubota et al. show that bacteria can use their filamentous phage to outcompete other bacteria, but increased phage production enables the evolution of cheater miniphages with truncated genomes. Miniphages exploit full-length phages and lower total phage production, causing some bacteria to lose their prophages and any associated fitness benefits.

The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain ...

Bacteriophages are rich in genetic diversity, due to frequent horizontal transfer and recombination. This makes traditional microbial phylogenetic analyses, often based on the assumption of vertical inheritance, not suitable for interpreting this diversity. Here, inspired by recent work on bacterial pangenomes, we investigate the evolution of a collection of 3425 actinobacteriophage genomes. We find that synteny is strongly conserved: core genes have a well-defined order, and most accessory genes are localized in a few locations along the core genome backbone. Within the core genome alignment, linkage disequilibrium decays rapidly with distance in some groups, while phylogenetic structure in other groups causes long-range linkage. Our quantitative characterizations extend across many groups of phages and indicate widespread homologous recombination restricted by strong gene order conservation. ### Competing Interest Statement The authors have declared no competing interest. National Science Foundation, https://ror.org/021nxhr62, PHY-2309135 Gordon and Betty Moore Foundation, https://ror.org/006wxqw41, 2919.02 Chan Zuckerberg Initiative (United States), https://ror.org/02qenvm24, DAF grant to the Kavli Institute for Theoretical Physics (KITP) Swiss National Science Foundation, https://ror.org/00yjd3n13, 310030_188547

The authors examine several defense systems and find that increased expression enhances their protection range, albeit at a cost of autoimmunity.