Bacteriophages (phages) are obligate parasites that use host bacterial translation machinery to produce viral proteins. However, some phages have alternative genetic codes with reassigned stop codons that are predicted to be incompatible with bacterial translation systems. We analysed 9,422 phage genomes and found that stop-codon recoding has evolved in diverse clades of phages that infect bacteria present in both human and animal gut microbiota. Recoded stop codons are particularly over-represented in phage structural and lysis genes. We propose that recoded stop codons might function to prevent premature production of late-stage proteins. Stop-codon recoding has evolved several times in closely related lineages, which suggests that adaptive recoding can occur over very short evolutionary timescales.

噬菌体（噬菌体）是专性寄生虫，使用宿主细菌翻译机器产生病毒蛋白。然而，一些噬菌体具有替代遗传密码和重新分配的终止密码子，预计这些密码子与细菌翻译系统不兼容。我们分析了 9,422 个噬菌体基因组，发现终止密码子重新编码已经在不同的噬菌体进化枝中进化，这些噬菌体感染存在于人类和动物肠道微生物群中的细菌。重新编码的终止密码子在噬菌体结构和裂解基因中特别多。我们建议重新编码的终止密码子可能起到防止后期蛋白质过早产生的作用。终止密码子重新编码在密切相关的谱系中已经进化了几次，这表明自适应重新编码可以在非常短的进化时间尺度内发生。