Diversity and evolution of the emerging Pandoraviridae family

Abstract

With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used 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 reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses 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 suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes.

Evidence of a Cellulosic Layer in Pandoravirus massiliensis Tegument and the Mystery of the Genetic Support of Its Biosynthesis

“…Given the lack of any bcsA domain in the orthologs of the ORF594 in other pandoraviruses and the lack of knowledge on the hypothetical proteins encoded by pandoraviruses, we could alternatively hypothesize that the virus could use for the synthesis of its particles tegument, the gene of the cellulose synthase of A. castellanii (Clarke et al, 2013). In a previous work, it has been shown that when Acanthamoeba was infected with a mimivirus, the transcription of the ameba felt dramatically and at 6 h after infection, the transcription became undetectable (Legendre et al, 2010). We observed herein, that the host gene of cellulose synthase was transcribed during the all the replication cycle of P. massiliensis, showing that the transcription of this amoebal gene is not impacted by the infection with Pandoravirus.…”

Hidden diversity of soil giant viruses

“…3a ; Supplementary Fig. 1 ) 8 , 44 . With the presence of 10 ancestral NCLDV genes, a number similar to several other NCLDV, the sylvanvirus genome can be considered near complete (Supplementary Fig.…”

Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes

“…Finally, we do expect that the physiological traits shared by these viruses will make their global gene contents qualitatively similar. Members of the same virus family should then appear well clustered in a cladistic analysis/tree [ 51 , 62 ].…”

“…The prefix “Meta” indicates sequences from nonisolated viruses. A more generic phylogenetic tree placing the Mimiviridae in the context of other large DNA virus families is shown in [ 51 ].…”