Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

Abstract

Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections, but also offering novel insights into pathogen genetics and evolution. A prominent example are cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative non-pathogenic relatives, such as M. smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate sub-cluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host-ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with M. leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, sub-cluster K1 mycobacteriophages are able to integrate into the genomes of M. abscessus and M. marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance.

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

“…In addition, based on the RSCU values of different species, we constructed the relationship between different Amanita and found that the relationship between different species based on RSCU was different from the sequence-based relationships. However, the genetic relationship between some species was correctly interpreted according to the RSCU value, which was consistent with other studies ( Crane et al, 2021 ; Gupta et al, 2021 ). The results show that the phylogenetic results based on RSCU can be an important supplement to the phylogenetic results based on sequence.…”

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

“…The relative synonymous codon usage (RSCU) of a range of Ganoderma species and strains was evaluated to identify relationships between them, which diverged from those established from sequence-based data. The RSCU value also accurately reflected the genetic connections between or within some Ganoderma strains or species, which was consistent with the findings of previous studies (Crane et al, 2021;Gupta et al, 2021;Li et al, 2022d). In general, this research has improved our understanding of codon usage characteristics and genetic evolution of this higher fungal group and other related fungal species.…”

Computational Prediction of Bacteriophage Host Ranges

“…For example, viruses frequently corrupt the translational machinery of their hosts to synthesize their own viral proteins [28], and this synthesis is generally more efficient if the codon usage patterns of the virus matches that of its host [29,30]. Taking advantage of this relationship, Crane, Versoza and colleagues [31] determined the codon usage bias of 129 mycobacteriophages across 14 putative mycobacterial hosts using COUSIN [32] to obtain important insights into putative mycobacterial host ranges in nature. Bacteriophage genomes can also acquire molecular characteristics of their hosts due to exposure to similar genome-wide mutational pressures, a process referred to as 'genome amelioration' [33][34][35].…”