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Viruses
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Genomics of Giant Viruses
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Genomics of Giant Viruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 9146

Special Issue Editor

Prof. Dr. Philippe Colson

E-Mail Website
Guest Editor
IRD, AP-HM, MEPHI, Aix Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
Interests: sequence analysis; clinical microbiology; antimicrobial resistance; diagnostic microbiology; molecular microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The giant viruses discovered in 2003 have since been shown to be common in our biosphere. Their genetic diversity has expanded considerably, and sequences closest to those of giant viruses are frequently and sometimes abundantly found in metagenomes, potentially leading to the assembly of complete genomes. However, some isolated giant viruses have a genome sufficiently divergent to escape such detections based on similarity searches. This suggests that knowledge on the diversity of giant viruses is still rather incomplete. Analyses of the genomes of giant viruses revealed a complexity similar to that of small cellular organisms, with characteristics that distinguish them from classical viruses, including genes that are hallmarks of cellular organisms. In addition, they demonstrate the significant mosaicism of these genomes resulting from numerous transfers of sequences and integration events as well as considerable proportions of ORFans. These various features make the genomics of giant viruses, that we are addressing in this Special Issue, a hot topic in the field of evolutionary biology.

Prof. Dr. Philippe Colson
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • giant virus
  • mimivirus
  • genomes
  • lateral sequence transfers
  • mosaicism
  • ORFans
  • evolution
  • classification

Published Papers (2 papers)

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Research

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13 pages, 4050 KiB  
Article
ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data
by Frank O. Aylward and Mohammad Moniruzzaman
Viruses 2021, 13(2), 150; https://doi.org/10.3390/v13020150 - 20 Jan 2021
Cited by 27 | Viewed by 4848
Abstract
Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs [...] Read more.
Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in ‘omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall. Full article
(This article belongs to the Special Issue Genomics of Giant Viruses)
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Review

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21 pages, 3203 KiB  
Review
A Brief History of Giant Viruses’ Studies in Brazilian Biomes
by Paulo Victor M. Boratto, Mateus Sá M. Serafim, Amanda Stéphanie A. Witt, Ana Paula C. Crispim, Bruna Luiza de Azevedo, Gabriel Augusto P. de Souza, Isabella Luiza M. de Aquino, Talita B. Machado, Victória F. Queiroz, Rodrigo A. L. Rodrigues, Ivan Bergier, Juliana Reis Cortines, Savio Torres de Farias, Raíssa Nunes dos Santos, Fabrício Souza Campos, Ana Cláudia Franco and Jônatas S. Abrahão
Viruses 2022, 14(2), 191; https://doi.org/10.3390/v14020191 - 19 Jan 2022
Cited by 4 | Viewed by 3069
Abstract
Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle [...] Read more.
Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil. Full article
(This article belongs to the Special Issue Genomics of Giant Viruses)
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