Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia.
Int J Mol Sci. 2021 Sep 26;22(19):10350. doi: 10.3390/ijms221910350.
phage MD8 is a temperate phage isolated from the freshwater lake Baikal. The organisation of the MD8 genome resembles the genomes of lambdoid bacteriophages. However, MD8 gene and protein sequences have little in common with classified representatives of lambda-like phages. Analysis of phage genomes revealed a group of other phages related to phage MD8 and the genomic layout of MD8-like phages indicated extensive gene exchange involving even the most conservative proteins and leading to a high degree of genomic mosaicism. Multiple horizontal transfers and mosaicism of the genome of MD8, related phages and other λ-like phages raise questions about the principles of taxonomic classification of the representatives of this voluminous phage group. Comparison and analysis of various bioinformatic approaches applied to λ-like phage genomes demonstrated different efficiency and contradictory results in the estimation of genomic similarity and relatedness. However, we were able to make suggestions for the possible origin of the MD8 genome and the basic principles for the taxonomic classification of lambdoid phages. The group comprising 26 MD8-related phages was proposed to classify as two close genera belonging to a big family of λ-like phages.
噬菌体 MD8 是从贝加尔湖淡水湖中分离出来的一种温和噬菌体。MD8 基因组的组织类似于 lambdoid 噬菌体的基因组。然而，MD8 基因和蛋白质序列与分类的 lambda 样噬菌体代表几乎没有共同之处。对噬菌体基因组的分析揭示了一组与噬菌体 MD8 相关的其他噬菌体，而 MD8 样噬菌体的基因组布局表明，广泛的基因交换涉及甚至最保守的蛋白质，导致基因组高度镶嵌。MD8、相关噬菌体和其他 λ 样噬菌体的基因组的多次水平转移和镶嵌提出了关于这个庞大噬菌体群体代表的分类学分类原则的问题。对 λ 样噬菌体基因组应用的各种生物信息学方法的比较和分析表明，在估计基因组相似性和相关性方面，效率不同，结果相互矛盾。然而，我们能够对 MD8 基因组的可能起源和 lambdoid 噬菌体的分类学分类的基本原则提出建议。建议将包含 26 个 MD8 相关噬菌体的群体分为两个密切相关的属，它们属于一个大的 λ 样噬菌体家族。
