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

Molecular characterization and expression analysis of interleukin-1 beta in Japanese eel (Anguilla japonica)

Interleukin 1-beta (IL-1B) is a key proinflammatory cytokine involved in disease resistance. In recent years, il-1β genes from several teleosts have been cloned. The Japanese eel (Anguilla japonica) is an evolutionarily primitive fish widely farmed in East Asia. The il-1β gene has not yet been cloned from Japanese eel. In this study, the complete cDNA of il-1β was successfully sequenced from peripheral leukocytes through the rapid amplification of cDNA ends. The il-1β gene consists of five exons and four introns, and the full-length cDNA spans 1204 bp, comprising a 99-bp 5' untranslated region, a 750-bp coding sequence, and a 355-bp 3' untranslated region. The deduced amino acid sequence includes a consensus IL-1 family signature but lacks both a signal peptide and an IL-1 converting enzyme cleavage site, similar to other teleost IL-1B proteins. Homology analysis revealed that Japanese eel IL-1B is highly conserved within the order Anguilliformes, sharing the highest similarity with American eel (Anguilla rostrata), followed by conger eel (Conger myriaster). Tissue expression analysis showed that il-1β is constitutively expressed in multiple tissues, with high expression in peripheral leukocytes and the spleen; moderate expression in the gill, liver, head kidney, trunk kidney, and intestine; and low expression in the heart, stomach, skin, and muscle. In vitro stimulation with zymosan, polyinosinic-polycytidylic acid, and lipopolysaccharide upregulated il-1β expression in peripheral leukocytes.

Diversity, evolution, and emergence of fish viruses

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.

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

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.

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

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.