Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method

Zhang, Wenjie; Wang, Ran; Gu, Chunping; Yang, Qian; He, Manli; Xiao, Wudian; He, Lvqin; Zhao, Mingde; Zou, Xiaojuan; Yu, Zehui

doi:10.1016/j.virusres.2023.199163

Cited by 3 publications

(2 citation statements)

References 33 publications

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“…Proteomic trees are expected to largely reflect evolutionary histories, although they are affected by some limitations. These include the challenge of reliably detecting remote homologies among proteins and the noise introduced by horizontal gene transfer (Adriaenssens et al., 2015; Chibani et al., 2019; Medvedeva et al., 2023; Rohwer & Edwards, 2002; Zhang et al., 2023). We downloaded the reference prokaryotic and eukaryotic virus trees from the GenomeNet/ViPTree server.…”

Section: Resultsmentioning

confidence: 99%

Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts

Forni,

Pozzoli,

Cagliani

et al. 2024

Molecular Ecology

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The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod‐infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral‐encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria‐infecting phages resulted to be significantly CpG‐depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG‐rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.

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Section: Resultsmentioning

confidence: 99%

Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts

Forni,

Pozzoli,

Cagliani

et al. 2024

Molecular Ecology

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“…The Alloherpesviridae are a family of large double-stranded viruses that infect fish and amphibians. Almost all members of the fish-infecting genera, Cyprinivirus, Salmonivirus, Ictalurivirus , have been associated with disease outbreaks ( 127 ). Notable among the Alloherpesviridae is Cyprinid herpesvirus-3 (CyHV-3), also known as koi herpesvirus, that has caused severe disease in common carp in Europe, the Middle East, Africa, Asia, and North America ( 61 ).…”

Section: Diversity and Evolution Of Fish Virusesmentioning

confidence: 99%

Diversity, evolution, and emergence of fish viruses

Costa,

Holmes

2024

J Virol

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The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.

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VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data

Fu,

Wu,

Zhang

et al. 2023

Briefings in Bioinformatics

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Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn’s disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.

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Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method

Cited by 3 publications

References 33 publications

Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts

Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts

Diversity, evolution, and emergence of fish viruses

VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data

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