Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages

Pseudomonas 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 Pseudomonas 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 lambda-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 lambda-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 lambda-like phages.

Automated summary

The genome of Pseudomonas phage MD8 exhibits extensive gene exchange and mosaic patterns with other lambda-like phages, challenging taxonomic classification principles. Multiple horizontal transfers and genomic mosaicism raise questions about the relatedness of MD8 and similar phages, leading to contradictory results in bioinformatics analysis. Suggestions for the origin of MD8 genome and taxonomic classification principles were made based on comparison of different bioinformatic approaches applied to lambda-like phage genomes.