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Genomes of a Novel Group of Phages That Use Alternative Genetic Code Found in Human Gut Viromes

Igor Babkin1,2, Artem Tikunov1,2, Vera Morozova1

  • 1Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.

International Journal of Molecular Sciences
|October 28, 2023
PubMed

Insights

A novel phage genome (phAss-1) with unusual genetic code was discovered in the human gut virome. This finding highlights the need for diverse translation tables in phage genome analysis and data deposition.

Area of Science:

  • Microbiology
  • Virology
  • Bioinformatics

Background:

  • Metagenomics enables phage genome detection in microbial communities.
  • Alternative genetic codes in phages hinder accurate genome analysis.
  • The human gut virome is a rich source of microbial diversity.

Purpose of the Study:

  • To report the discovery and characterization of a novel phage genome with an unusual genetic code.
  • To investigate the implications of alternative genetic codes for phage genome analysis.
  • To establish a new phage genus based on genomic similarities.

Main Methods:

  • De novo assembly of human gut virome data.
  • Genome analysis of identified phage sequences.
  • Comparative genomics and phylogenetic analysis.
  • Identification of suppressor tRNA genes and non-canonical stop codons.

Main Results:

  • Discovery of the unusual phage genome phAss-1 (135,976 bp) in the human gut virome.
  • Identification of 41 ORFs with TAG stop codons and three suppressor tRNA genes in phAss-1.
  • Detection of two similar phage genomes (BK046881_ctckW2, BK025033_ct6IQ4) in metagenomic data.
  • Genomic and phylogenetic analyses support the proposal of a new genus, *Phassvirus*.

Conclusions:

  • The discovery of phAss-1 and related phages necessitates the use of alternative translation tables for accurate phage genome analysis.
  • The proposed *Phassvirus* genus represents a distinct lineage of phages with unique genetic features.
  • Accurate phage genome deposition in databases requires consideration of diverse translation systems.
Keywords:
bacteriophagecaudoviricetesgenome sequencephylogeneticsstop codon recodingvirus taxonomy

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