Phages can fundamentally alter the physiology and metabolism of their hosts. While ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception in the APSE phage that is found associated with the gammaproteobacterial Hamiltonella defensa, hosted by several insect species. This secondary facultative endosymbiont is not necessary for the survival of its hosts but can infect certain individuals or even whole populations. Its infection in aphids is often associated with protection against parasitoid wasps. This protective phenotype has actually been linked to the infection of the symbiont strain with an APSE, which carries a toxin cassette that varies among so-called "types". In the present work, we seek to expand our understanding of the diversity of APSE phages as well as the relations of their Hamiltonella hosts. For this, we assembled and annotated the full genomes of 16 APSE phages infecting Hamiltonella symbionts across 10 insect species. Molecular and phylogenetic analyses suggest that recombination has occurred repeatedly among lineages. Comparative genomics of the phage genomes revealed two variable regions that are useful for phage typing. Additionally, we find that mobile elements could play a role in the acquisition of new genes in the toxin cassette. Altogether, we provide an unprecedented view of APSE diversity and their genome evolution across aphids. This genomic investigation will provide a valuable resource for the design and interpretation of experiments aiming at understanding the protective phenotype these phages confer to their insect hosts.

中文翻译：

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内在的保护者：跨越蚜虫的APSE噬菌体的比较基因组学揭示了猖Rec的重组和多样化的毒素库。

噬菌体可以从根本上改变宿主的生理和新陈代谢。尽管它们在细菌界无处不在，但很少在共生细菌中被描述。在APSE噬菌体中发现的一个显着例外是，它与由几种昆虫寄主的γ-变形细菌汉密尔顿氏菌相关。继发性兼性内共生不是其宿主存活所必需的，但是可以感染某些个体甚至整个人群。它在蚜虫中的感染通常与对寄生性黄蜂的保护有关。实际上，这种保护性表型与共生菌株被APSE感染有关，APSE携带着毒素盒，这种毒素盒在所谓的“类型”之间有所不同。在目前的工作中，我们寻求扩大对APSE噬菌体多样性及其汉密尔顿杆菌宿主之间关系的理解。为此，我们组装并注释了16种APSE噬菌体的完整基因组，这些噬菌体感染了10个昆虫物种的汉密尔顿共生菌。分子和系统发育分析表明重组已经在宗族之间反复发生。噬菌体基因组的比较基因组学揭示了两个可用于噬菌体分型的可变区。此外，我们发现移动元件可能在毒素盒中新基因的获取中发挥作用。总之，我们提供了APSE多样性及其在蚜虫中的基因组进化的前所未有的视图。