File S4 (separate file). Detailed wGRR matrix cluster classification for each P4-like element from To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli, sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, since almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

噬菌体（Bacteriophages，简称phages）是细菌的寄生物，而它们自身也可被噬菌体卫星（phage satellites）寄生。目前学界对卫星劫持噬菌体的分子机制已有较为深入的解析，但这类遗传元件的起源、丰度、分布与组成却鲜为人知。本研究表明，类P4元件（P4-like elements）在超过30%的肠杆菌目（Enterobacterales）基因组中存在，在大肠杆菌（Escherichia coli）基因组中的占比接近半数，且有时会以多个不同拷贝的形式出现。我们共鉴定出1000余个类P4元件，其核心基因组的遗传组织高度保守，同时存在少数携带高度可变基因的热点区域。这类元件从未在质粒（plasmid）中被发现，且与已知噬菌体的同源性极低，提示其拥有独立的进化起源。与之相反，类P4元件分散分布于细菌染色体中，这可能是因为其整合酶（integrase）常与其他元件发生交换。劫持功能的有根系统发育树具有相关性，暗示二者长期存在协同进化关系。研究还揭示类P4元件具有广泛的宿主范围：几乎完全相同的元件可在不同细菌属中被检测到。本研究结果表明，类P4噬菌体卫星构成了一类极为独特、分布广泛且起源古老的可移动遗传元件（mobile genetic elements），为研究噬菌体与其卫星之间拮抗互作的分子进化开辟了新的研究方向。本文属于《微生物可移动遗传元件的隐秘生命》（'The secret lives of microbial mobile genetic elements'）专题特刊的一部分。