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Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae
The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of vi...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005611/ https://www.ncbi.nlm.nih.gov/pubmed/33790885 http://dx.doi.org/10.3389/fmicb.2021.657471 |
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author | Karki, Sangita Moniruzzaman, Mohammad Aylward, Frank O. |
author_facet | Karki, Sangita Moniruzzaman, Mohammad Aylward, Frank O. |
author_sort | Karki, Sangita |
collection | PubMed |
description | The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with > 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists. |
format | Online Article Text |
id | pubmed-8005611 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-80056112021-03-30 Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae Karki, Sangita Moniruzzaman, Mohammad Aylward, Frank O. Front Microbiol Microbiology The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with > 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists. Frontiers Media S.A. 2021-03-15 /pmc/articles/PMC8005611/ /pubmed/33790885 http://dx.doi.org/10.3389/fmicb.2021.657471 Text en Copyright © 2021 Karki, Moniruzzaman and Aylward. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Karki, Sangita Moniruzzaman, Mohammad Aylward, Frank O. Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae |
title | Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae |
title_full | Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae |
title_fullStr | Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae |
title_full_unstemmed | Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae |
title_short | Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae |
title_sort | comparative genomics and environmental distribution of large dsdna viruses in the family asfarviridae |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005611/ https://www.ncbi.nlm.nih.gov/pubmed/33790885 http://dx.doi.org/10.3389/fmicb.2021.657471 |
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