Evolution and Phylogeny of Large DNA Viruses, Mimiviridae and Phycodnaviridae Including Newly Characterized Heterosigma akashiwo Virus

Abstract

Nucleocytoplasmic DNA viruses are a large group of viruses that harbor double-stranded DNA genomes with sizes of several 100 kbp, challenging the traditional concept of viruses as small, simple ‘organisms at the edge of life.’ The most intriguing questions about them may be their origin and evolution, which have yielded the variety we see today. Specifically, the phyletic relationship between two giant dsDNA virus families that are presumed to be close, Mimiviridae, which infect Acanthamoeba, and Phycodnaviridae, which infect algae, is still obscure and needs to be clarified by in-depth analysis. Here, we studied Mimiviridae–Phycodnaviridae phylogeny including the newly identified Heterosigma akashiwo virus strain HaV53. Gene-to-gene comparison of HaV53 with other giant dsDNA viruses showed that only a small proportion of HaV53 genes show similarities with the others, revealing its uniqueness among Phycodnaviridae. Phylogenetic/genomic analysis of Phycodnaviridae including HaV53 revealed that the family can be classified into four distinctive subfamilies, namely, Megaviridae (Mimivirus-like), Chlorovirus-type, and Coccolitho/Phaeovirus-type groups, and HaV53 independent of the other three groups. Several orthologs found in specific subfamilies while absent from the others were identified, providing potential family marker genes. Finally, reconstruction of the evolutionary history of Phycodnaviridae and Mimiviridae revealed that these viruses are descended from a common ancestor with a small set of genes and reached their current diversity by differentially acquiring gene sets during the course of evolution. Our study illustrates the phylogeny and evolution of Mimiviridae–Phycodnaviridae and proposes classifications that better represent phyletic relationships among the family members.

Giant Viruses – Big Surprises

“…Iridoviridae, Poxviridae, Asfarviridae, and Ascoviridae [39,40], for which a common ancestor had 113 been proposed [41,42]. smaller ancestral viruses carrying only a few dozens of genes, and through gene duplications and horizontal gene transfer (HGT), have rapidly expanded and diversified [44,[47][48][49]. This model agrees with metagenomic studies and the wave of giant virus discoveries in recent years (e.g.…”

Metagenomic analysis of virus diversity and relative abundance in a eutrophic freshwater harbour

“…There is evidence that some viruses previously and tentatively considered phycodnaviruses (i.e., members of the Phycodnaviridae family) are more closely related to Mimiviridae than Phycodnaviridae , and in fact form a separate subfamily ‘Mesomimivirinae’ within the Mimiviridae [39]. Though not formally recognized by the International Committee for Taxonomy of Viruses (ICTV), several publications have used the terms ‘ Megaviridae ’ or ‘extended Mimiviridae ’ to refer to ‘Mesomimivirinae’ [40]. Here we will use the term Mimiviridae to encompass the formally recognized Mimiviridae as well as the proposed ‘extended Mimiviridae ’ subfamily that are often considered phycodnaviruses.…”

Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses

“…S13 ), the longest contigs from the v21821 cluster, along with PoV-01B could be clearly attributed to mesomimiviruses. In these analyses, the sole long contig from the second cluster showed more affinity to the Phycodnaviridae , and in particular to Raphidovirus , a virus with a unique position among the members of the family 51 . Finally, phylogenetic analysis of highly conserved genes placed PoV-01B well among the v21821-cluster contigs and the whole clade, again within the mesomimiviruses ( Fig.…”