Hodor megaplasmids

Genomes of (1) curated Hodor genomes (Hodor.38.genomes), (2) draft Hodor genomes (draft.Hodor.genomes.tar.gz), (3) the inserted complete, intact prophage genomes (Hodor.prophages), and (4) (pro)phage sequences highly similar to Hodor-associated prophages (prophage01.all.pure, prophage02.all.pure, and prophage03.all.pure; note that some of these were with host fractions, which were determined and removed using CheckV). Manuscript informationTitle: A distinct class of conjugative megaplasmids includes potential vehicles for prophage disseminationAuthors: Ling Yuan (袁凌), Yiting Qin (秦祎婷), Jacob West-Roberts, Karthik Anantharaman, Haoyu Wang (王浩宇), Yuanqiang Zou (邹远强), Yi Duan (段屹), Antonio Pedro Camargo*, Eugene V. Koonin*, LinXing Chen (陈林兴)*Abstract: Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.