crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.

中文翻译：

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裂殖体病毒在基因水平上的进化研究。

类crAss病毒是最近发现的细菌噬菌体家族。进化枝的缩写叫crAssphage，是一种肠噬菌体，估计存在于至少一半的人口中，它构成了某些人类粪便病毒宏基因组学数据集中高达90％的序列。我们专注于crAssphage基因组上编码的基因的进化动力学。通过研究基因的保守性，发现不同功能组之间进化速率的一致性变化。在crAss样基因组中检测到基因重复。通过探索基因功能类别之间的差异，我们确认了编码衣壳蛋白的基因是最普遍存在的，尽管它们的总体序列保守性较低。有可能鉴定出其进化树彼此密切相关的蛋白核心，表明它们的遗传相互作用。该组包括衣壳蛋白，因此衣壳蛋白被认为非常适合重建该病毒进化枝的系统树。显示了普遍存在与病毒蛋白序列保守性之间的负相关。总之，这项研究提供了有关crAss样病毒中不同基因进化的深入图片。