takeuchiETAL_table-S4_ESM.tsv from Prophages and plasmids can display opposite trends in the types of accessory genes they carry

Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.

移动遗传元件（Mobile Genetic Elements, MGEs），例如噬菌体与质粒，通常携带编码细菌功能的附属基因，进而推动细菌的演化进程。是否存在支配MGE所携带附属基因库的规律？若此类规律确实存在，则其可能体现在不同MGE所携带的附属基因类型中。为验证这一假说，本研究依托公共数据库，针对21种病原菌基因组中的前噬菌体与质粒，对比二者携带抗生素抗性基因（Antibiotic Resistance Genes, ARGs）与毒力因子基因（Virulence Factor Genes, VFGs）的频率差异。研究结果显示：相较于基因组背景，3个物种的前噬菌体携带VFGs的频率显著高于ARGs，而9个物种的质粒携带ARGs的频率则显著高于VFGs。在检测到前噬菌体-质粒差异的大肠杆菌中，前噬菌体携带的VFGs所编码的功能范围远窄于质粒携带的VFGs，通常涉及宿主细胞损伤或宿主免疫调控。在未观测到上述差异的物种中，前噬菌体与质粒几乎不携带ARGs与VFGs。上述结果表明，MGEs可根据自身感染策略差异化携带附属基因类型，这揭示了一条由MGE介导的水平基因转移的潜在规律。