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Journal of General Virology header logo Journal of General Virology

Volume 105, Issue 5

Decoding huge phage diversity: a taxonomic classification of Lak megaphages Open Access

Abstract

High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the ‘Grandevirales’. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order ‘Grandevirales’. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): lak , megaphage , phage genomics and phage taxonomy
Funding
This study was supported by the:
  • Medical Research Council (Award MR/L015080/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13636)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13635)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13634)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/X011011/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13633)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13631)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/X011054/1)
    • Principle Award Recipient: NotApplicable
  • Medical Research Council (Award MR/W031205/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/M009513/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/W015706/1)
    • Principle Award Recipient: NotApplicable
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-05-30
2025-05-23
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Decoding huge phage diversity: a taxonomic classification of Lak megaphages
J. Gen. Virol. 105, 001997 (2024); https://doi.org/10.1099/jgv.0.001997
/content/journal/jgv/10.1099/jgv.0.001997
/content/journal/jgv/10.1099/jgv.0.001997
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