Virus Genomics and Diversity

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (22 October 2024) | Viewed by 2067

Special Issue Editors


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Guest Editor
Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, USA
Interests: virus evolution, detection and discovery

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Guest Editor
Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Interests: viral metagenomics; coinfections; evolution; cross-species spillover of viruses
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Guest Editor
1. Department of Virology, College of Medicine, University of Ibadan, Oyo, Nigeria
2. Infectious Disease Institute, College of Medicine, University of Ibadan, Oyo, Nigeria
Interests: retro-, entero- and hepatitis viruses; virology

Special Issue Information

Dear Colleagues,

Our understanding of virus genomics and diversity has always been limited by available technology. Consequently, eras of virus discovery have been heralded by new technologies. The advent of multiple high-throughput genome sequencing technologies (Illumina, Nanopore, PacBio, and others) and the enhanced computing capacity now available have increased our resolution of virus diversity and simultaneously ushered in an era of virus discovery in both common and unusual places. The accompanying insights continue to expand our understanding of virus genome sizes, architecture, host range, and genotypes in both commonly explored and previously unexplored ecosystems.

In this Special Issue, we explore virus genomes and what they show us about the possibilities that exist. We welcome articles describing the use of any nucleotide sequencing technology to catalogue novel virus genomes (in terms of genome size, architecture, host range, families, species, and genotypes) in any sample type (environmental, vertebrate, or invertebrate hosts, reservoirs, healthy or diseased subjects) and/or ecosystem. Articles describing novel phage genomes are also welcome.

Dr. Temitope O. C. Faleye
Dr. Simona Kraberger
Dr. Moses Olubusuyi Adewumi
Guest Editors

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Keywords

  • genomics
  • diversity
  • virus evolution
  • virus detection
  • genome sequencing
  • DNA sequencing

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Published Papers (1 paper)

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Research

19 pages, 3235 KiB  
Article
Exploring Viral Interactions in Clavibacter Species: In Silico Analysis of Prophage Prevalence and Antiviral Defenses
by Lucía Margarita Rubí-Rangel, Josefina León-Félix and Claudia Villicaña
Life 2025, 15(2), 187; https://doi.org/10.3390/life15020187 - 27 Jan 2025
Viewed by 1559
Abstract
Clavibacter is a phytopathogenic genus that causes severe diseases in economically important crops, yet the role of prophages in its evolution, pathogenicity, and adaptation remains poorly understood. In this study, we used PHASTER, Prophage Hunter, and VirSorter2 to identify prophage-like sequences in publicly [...] Read more.
Clavibacter is a phytopathogenic genus that causes severe diseases in economically important crops, yet the role of prophages in its evolution, pathogenicity, and adaptation remains poorly understood. In this study, we used PHASTER, Prophage Hunter, and VirSorter2 to identify prophage-like sequences in publicly available Clavibacter genomes. Prophage predictions were checked by hand to make them more accurate. We identified 353 prophages, predominantly in chromosomes, with some detected phage-plasmids. Most prophages exhibited traits of advanced domestication, such as an unimodal genome length distribution, reduced numbers of integrases, and minimal transposable elements, suggesting long-term interactions with their bacterial hosts. Comparative genomic analyses uncovered high genetic diversity, with distinct prophage clusters showing species-specific and interspecies conservation patterns. Functional annotation revealed prophage-encoded genes were involved in sugar metabolism, heavy metal resistance, virulence factors, and antibiotic resistance, highlighting their contribution to host fitness and environmental adaptation. Defense system analyses revealed that, despite lacking CRISPR-Cas, Clavibacter genomes harbor diverse antiviral systems, including PD-Lambda-1, AbiE, and MMB_gp29_gp30, some encoded within prophages. These findings underscore the pervasive presence of prophages in Clavibacter and their role in shaping bacterial adaptability and evolution. Full article
(This article belongs to the Special Issue Virus Genomics and Diversity)
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