Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family

Abstract

Chrysochromulina ericina virus CeV-01B (CeV) was isolated from Norwegian coastal waters in 1998. Its icosahedral particle is 160 nm in diameter and encloses a 474-kb double-stranded DNA (dsDNA) genome. This virus, although infecting a microalga (the haptophyceae Haptolina ericina, formerly Chrysochromulina ericina), is phylogenetically related to members of the Mimiviridae family, initially established with the acanthamoeba-infecting mimivirus and megavirus as prototypes. This family was later split into two genera (Mimivirus and Cafeteriavirus) following the characterization of a virus infecting the heterotrophic stramenopile Cafeteria roenbergensis (CroV). CeV, as well as two of its close relatives, which infect the unicellular photosynthetic eukaryotes Phaeocystis globosa (Phaeocystis globosa virus [PgV]) and Aureococcus anophagefferens (Aureococcus anophagefferens virus [AaV]), are currently unclassified by the International Committee on Viral Taxonomy (ICTV). The detailed comparative analysis of the CeV genome presented here confirms the phylogenetic affinity of this emerging group of microalga-infecting viruses with the Mimiviridae but argues in favor of their classification inside a distinct clade within the family. Although CeV, PgV, and AaV share more common features among them than with the larger Mimiviridae, they also exhibit a large complement of unique genes, attesting to their complex evolutionary history. We identified several gene fusion events and cases of convergent evolution involving independent lateral gene acquisitions. Finally, CeV possesses an unusual number of inteins, some of which are closely related despite being inserted in nonhomologous genes. This appears to contradict the paradigm of allele-specific inteins and suggests that the Mimiviridae are especially efficient in spreading inteins while enlarging their repertoire of homing genes.IMPORTANCE Although it infects the microalga Chrysochromulina ericina, CeV is more closely related to acanthamoeba-infecting viruses of the Mimiviridae family than to any member of the Phycodnaviridae, the ICTV-approved family historically including all alga-infecting large dsDNA viruses. CeV, as well as its relatives that infect the microalgae Phaeocystic globosa (PgV) and Aureococcus anophagefferens (AaV), remains officially unclassified and a source of confusion in the literature. Our comparative analysis of the CeV genome in the context of this emerging group of algainfecting viruses suggests that they belong to a distinct clade within the established Mimiviridae family. The presence of a large number of unique genes as well as specific gene fusion events, evolutionary convergences, and inteins integrated at unusual locations document the complex evolutionary history of the CeV lineage.

Diversity and evolution of the emerging Pandoraviridae family

“…For ten years following the serendipitous discovery of the first giant virus (i.e. easily visible by light microscopy) Acanthamoeba polyphaga Mimivirus 1,2 , environmental sampling in search of other Acanthamoeba-infecting viruses only succeeded in the isolation of additional Mimivirus relatives, now forming the still expanding Mimiviridae family [3][4][5][6] . In 2013, we returned to the Chilean coastal area from which we previously isolated Megavirus chilensis 3 , the largest known Mimiviridae.…”

Giant Viruses and their mobile genetic elements: the molecular symbiotic hypothesis

“…The toxin-antitoxin systems (T-A) behave in a similar way as R-M systems and also tend to become addictive modules. In addition, most of GV genomes encode for numerous mobile homing endonucleases frequently associated with self-splicing introns and inteins (also known as protein introns) [9,32,33]. Homing endonucleases are mobile and selfish genes that are known to be invasive, sometimes promoting the «homing» of their cognate introns or inteins into empty sites by the mean of homologous recombination [34].…”

“…Finally, more enigmatic MGEs have been evidenced in Mimiviridae: the Major Interspersed Genomic Elements (MIGEs) [32,35]. These elements are composed of a single ORF encoding a protein with a zinc-finger motif preceded by a short piece of non-coding DNA.…”

“…Supporting this view, it's noteworthy that inteins and introns are most often inserted in conserved GV «core» genes that are known to be essential for the achievement of the virus cycle such as DNA polymerase, Ribonucleotide reductase, RNA polymerase or Capsid genes [33,[42][43][44]. Additionally, it was evidenced that the well-known strong site-specificity of the homing-endonuclease is relaxed in GV genomes allowing the inteins to be inserted at multiple sites, in different genes, widening their possible anti-viral effects [32]. These data support the view that the multiplication of introns or inteins in GV genomes are not simply the result of proliferation of selfish genetics elements.…”

Commensalism in theMimiviridaegiant virus family

“…As of today, the Mimiviridae family appears composed of several distinct subfamilies (1–10) one of which, the proposed Megamimivirinae (7,10,11), corresponds to the family members specifically infecting Acanthamoeba (1,3–5,8). Members of this subfamilies, collectively refers to as “mimiviruses” throughout this article, can be infected by dsDNA satellite viruses called virophages only able to replicate using the already installed intracytoplasmic viral factory (6,12–15).…”