Abstract
Faustovirus is a recently discovered genus of large DNA virus infecting the amoeba Vermamoeba vermiformis, which is phylogenetically related to Asfarviridae. To better understand the diversity and evolution of this viral group, we sequenced six novel Faustovirus strains, mined published metagenomic datasets and performed a comparative genomic analysis. Genomic sequences revealed three consistent phylogenetic groups, within which genetic diversity was moderate. The comparison of the major capsid protein (MCP) genes unveiled between 13 and 18 type-I introns that likely evolved through a still-active birth and death process mediated by intron-encoded homing endonucleases that began before the Faustovirus radiation. Genome-wide alignments indicated that despite genomes retaining high levels of gene collinearity, the central region containing the MCP gene together with the extremities of the chromosomes evolved at a faster rate due to increased indel accumulation and local rearrangements. The fluctuation of the nucleotide composition along the Faustovirus (FV) genomes is mostly imprinted by the consistent nucleotide bias of coding sequences and provided no evidence for a single DNA replication origin like in circular bacterial genomes.
Highlights
The nucleo-cytoplasmic large DNA viruses (NCLDVs) comprise an expansive and very diverse group of viruses that infect a variety of eukaryotes
Most of the NCLDVs replicate in the cytoplasm of infected cells and share several core genes encoding proteins involved in virus morphogenesis and replication
The nucleotide frequencies at the first and second codon positions, which determine the nature of the encoded amino acid, are under stronger selective constraints. These results indicate that the variation in the nucleotide frequency across these viral genomes is mostly driven by the distribution of protein genes between the two DNA strands, owing to a relatively consistent compositional bias in coding sequences, potentially resulting from a combination of mutational biases and selective pressures
Summary
The nucleo-cytoplasmic large DNA viruses (NCLDVs) comprise an expansive and very diverse group of viruses that infect a variety of eukaryotes [1] They are especially notorious because they include the so called giant viruses, with genome sizes exceeding those of many cellular organisms [2]. Most of the NCLDVs replicate in the cytoplasm of infected cells and share several core genes encoding proteins involved in virus morphogenesis and replication. Among NCLDVs, the proposed Faustovirus (FV) genus comprises large DNA viruses isolated using the free-living model amoeba Vermamoeba vermiformis (VV) as a host [7]. Their capsids are icosahedral, and their virions are 200–240 nm large [8].
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