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Comparative Study
. 2024:2802:427-453.
doi: 10.1007/978-1-0716-3838-5_14.

Comparative Analyses of Bacteriophage Genomes

Fernando Pacheco Nobre Rossi  1 , Vinicius Sousa Flores  1 , Guillermo Uceda-Campos  1 , Deyvid Emanuel Amgarten  2 , João Carlos Setubal  1 , Aline Maria da Silva  3
Affiliations
Comparative Study

Comparative Analyses of Bacteriophage Genomes

Fernando Pacheco Nobre Rossi et al. Methods Mol Biol. 2024.

Abstract

Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.

Keywords: Bioinformatics; Comparative genomics; Functional annotation; Phage; Phage clustering; Prophage.

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References

    1. Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, Weitz JS (2021) Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol 19:501–513. https://doi.org/10.1038/s41579-021-00530-x - DOI - PubMed
    1. Łoś J, Zielińska S, Krajewska A, Michalina Z, Małachowska A, Kwaśnicka K, Łoś M (2021) Temperate phages, prophages, and lysogeny. In: Harper DR, Abedon ST, Burrowes BH, McConville ML (eds) Bacteriophages: biology, technology, therapy. Springer International Publishing, Cham, pp 119–150. https://doi.org/10.1007/978-3-319-41986-2_3 - DOI
    1. Touchon M, Moura de Sousa JA, Rocha EPC (2017) Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr Opin Microbiol 38:66–73. https://doi.org/10.1016/j.mib.2017.04.010 - DOI - PubMed
    1. Dion MB, Oechslin F, Moineau S (2020) Phage diversity, genomics and phylogeny. Nat Rev Microbiol 18:125–138. https://doi.org/10.1038/s41579-019-0311-5 - DOI - PubMed
    1. Parikka KJ, Le Romancer M, Wauters N, Jacquet S (2017) Deciphering the virus-to-prokaryote ratio (VPR): insights into virus–host relationships in a variety of ecosystems. Biol Rev 92:1081–1100. https://doi.org/10.1111/brv.12271 - DOI - PubMed

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