Diversity and evolution of the emerging Pandoraviridae family

Abstract

With DNA genomes up to 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting Pandoraviruses remained the most spectacular viruses since their description in 2013. Our isolation of three new strains from distant locations and environments allowed us to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses, led to the discovery of many non-coding transcripts while significantly reducing the former set of predicted protein-coding genes. We found that the Pandoraviridae exhibit an open pan genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggests that de novo gene creation is a strong component in the evolution of the giant Pandoravirus genomes.

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

“…Mobile genetic elements (MGEs) are a crucial component of the living world, being the major vehicles for horizontal gene transfer (HGT; Koonin and Wolf, ), agents of genomic recombination (Cossu et al ., ) and cradles of novel genes (Keller et al ., ; Forterre and Gaïa, ; Legendre et al ., ). Whereas archaea are much more closely related to eukaryotes than to bacteria in terms of fundamental molecular mechanisms (replication, transcription and translation), the set of MGEs (mobilome) infecting archaea and bacteria are strikingly similar and very different from those present in eukaryotes (Forterre, ; Forterre et al ., ).…”

The DNA Methylation Landscape of Giant Viruses

“…According to the presence/absence of pseudogenes in the other strains, as detected using tblastn, we designed a putative evolutionary scenario for each of these genes (see Table S2). As previously discussed for pandoraviruses (37,47), the process of de novo gene creation seems to participate to the shaping of Cedratviruses genomes. Interestingly, among the 51 genes unique to C. kamchatka only one has a clear predicted function: the ck412 DNA MTase.…”

“…The first family of giant viruses to be discovered, the Mimiviridae, have megabase-sized AT-rich linear genomes packaged in icosahedral capsids (21)(22)(23). In contrast, the Pandoraviruses have GC-rich linear genomes, twice as big with up to 2.5 Mb, packaged in amphora-shaped capsids (29,37). Again different, Pithoviruses (26) and Cedratviruses (27,38) have smaller circular AT-rich genomes, ranging from 400 to 700 Mb, and packaged in the largest known amphora-shaped capsids.…”

“…We analyzed two distinct Mimiviridae and their associated transpovirons as well as a virophage (45). We also surveyed a Marseilleviridae (46), five distinct Pandoraviruses (29,37,47), a Mollivirus (48) and a Pithovirus (26). Finally, we isolated a new Cedratvirus (Cedratvirus kamchatka) that we sequenced using SMRT sequencing to assess its methylome.…”

Frontiers in antiviral therapy and immunotherapy

“…11 Another is the ancient lineage of nucleocytosolic large DNA viruses (NCLDVs), which are emerging human pathogens that possess enormous genomes of up to several megabases in size encoding hundreds of proteins with unique and unknown functions. 12 Moreover, hundreds of human-and avian-infective viruses such as IAV strain H5N1 are known, but recent efforts indicate the true number may be in the millions and many harbour zoonotic potential. 13 It is increasingly clear that host-virus interactions have generated truly vast yet poorly understood and untapped biodiversity.…”