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Pandoraviruses are highly derived phycodnaviruses.

Yutin N, Koonin EV - Biol. Direct (2013)

Bottom Line: Pandoraviruses show a distant relationship with other nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes, lack some of the NCLDV core genes and in particular do not appear to be specifically related to the other, better characterized family of giant viruses, the Mimiviridae.Here we report phylogenetic analysis of 6 core NCLDV genes that confidently places Pandoraviruses within the family Phycodnaviridae, with an apparent specific affinity with Coccolithoviruses.We conclude that, despite their many unusual characteristics, Pandoraviruses are highly derived phycodnaviruses.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. koonin@ncbi.nlm.nih.gov.

ABSTRACT
The recently discovered Pandoraviruses are by far the largest viruses known, with their 2 megabase genomes exceeding in size the genomes of numerous bacteria and archaea. Pandoraviruses show a distant relationship with other nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes, lack some of the NCLDV core genes and in particular do not appear to be specifically related to the other, better characterized family of giant viruses, the Mimiviridae. Here we report phylogenetic analysis of 6 core NCLDV genes that confidently places Pandoraviruses within the family Phycodnaviridae, with an apparent specific affinity with Coccolithoviruses. We conclude that, despite their many unusual characteristics, Pandoraviruses are highly derived phycodnaviruses. These findings imply that giant viruses have independently evolved from smaller NCLDV on at least two occasions.

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Maximum-Likelihood trees of DNA-directed RNA polymerase. A, alpha subunit. B, beta subunit. The designations are as in Figure 2.
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Figure 3: Maximum-Likelihood trees of DNA-directed RNA polymerase. A, alpha subunit. B, beta subunit. The designations are as in Figure 2.

Mentions: To gain further insight into the origin of the Pandoraviruses, we then performed phylogenetic analysis of the 17 ancestral NCLDV genes that are represented in the pandoravirus genomes. In 6 of the 17 phylogenetic trees, Pandoraviruses grouped within the Phycodnaviridae clade, or in cases when such a clade was absent, with members of the family Phycodnaviridae (Figures 2-3 and Additional file 2). In 10 of the remaining trees, the Pandoravirus genes clustered with eukaryotic homologs (Additional file 2), suggestive of replacement of ancestral NCLDV genes with homologs derived from the hosts, as observed for multiple genes in the previous phylogenomic analysis of the NCLDV [13]. Only the gene for the dual specificity phosphatase (NCVOG0040) showed an apparent phylogenetic affinity with NCLDV outside Phycodnaviridae, namely with Marseilleviruses (Additional file 2). Similar to several other genes in the ancestral NCLDV gene set [13], the tree for the dual specificity phosphatases shows NCLDV scattered among homologs from cellular life forms (Additional file 2). This pattern suggests that the evolution of the phosphatase gene in the NCLDV involved multiple gene transfers and replacements. One of such gene transfers might have involved the phosphatase genes of pandoravirus and marseillevirus. Additional intervirus gene transfers could have involved among non-ancestral viral genes as implied by the detection of 17 pandoravirus genes with best database hits to mimivirus homologs [6]. Gene exchange between diverse viruses infecting amoebae has been reported previously. Indeed, amoebal cell, with their omnivorous phagocytic life style have been recognized as “melting pots” of horizontal gene transfers, so such intervirus gene exchanges could be expected.


Pandoraviruses are highly derived phycodnaviruses.

Yutin N, Koonin EV - Biol. Direct (2013)

Maximum-Likelihood trees of DNA-directed RNA polymerase. A, alpha subunit. B, beta subunit. The designations are as in Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3924356&req=5

Figure 3: Maximum-Likelihood trees of DNA-directed RNA polymerase. A, alpha subunit. B, beta subunit. The designations are as in Figure 2.
Mentions: To gain further insight into the origin of the Pandoraviruses, we then performed phylogenetic analysis of the 17 ancestral NCLDV genes that are represented in the pandoravirus genomes. In 6 of the 17 phylogenetic trees, Pandoraviruses grouped within the Phycodnaviridae clade, or in cases when such a clade was absent, with members of the family Phycodnaviridae (Figures 2-3 and Additional file 2). In 10 of the remaining trees, the Pandoravirus genes clustered with eukaryotic homologs (Additional file 2), suggestive of replacement of ancestral NCLDV genes with homologs derived from the hosts, as observed for multiple genes in the previous phylogenomic analysis of the NCLDV [13]. Only the gene for the dual specificity phosphatase (NCVOG0040) showed an apparent phylogenetic affinity with NCLDV outside Phycodnaviridae, namely with Marseilleviruses (Additional file 2). Similar to several other genes in the ancestral NCLDV gene set [13], the tree for the dual specificity phosphatases shows NCLDV scattered among homologs from cellular life forms (Additional file 2). This pattern suggests that the evolution of the phosphatase gene in the NCLDV involved multiple gene transfers and replacements. One of such gene transfers might have involved the phosphatase genes of pandoravirus and marseillevirus. Additional intervirus gene transfers could have involved among non-ancestral viral genes as implied by the detection of 17 pandoravirus genes with best database hits to mimivirus homologs [6]. Gene exchange between diverse viruses infecting amoebae has been reported previously. Indeed, amoebal cell, with their omnivorous phagocytic life style have been recognized as “melting pots” of horizontal gene transfers, so such intervirus gene exchanges could be expected.

Bottom Line: Pandoraviruses show a distant relationship with other nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes, lack some of the NCLDV core genes and in particular do not appear to be specifically related to the other, better characterized family of giant viruses, the Mimiviridae.Here we report phylogenetic analysis of 6 core NCLDV genes that confidently places Pandoraviruses within the family Phycodnaviridae, with an apparent specific affinity with Coccolithoviruses.We conclude that, despite their many unusual characteristics, Pandoraviruses are highly derived phycodnaviruses.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. koonin@ncbi.nlm.nih.gov.

ABSTRACT
The recently discovered Pandoraviruses are by far the largest viruses known, with their 2 megabase genomes exceeding in size the genomes of numerous bacteria and archaea. Pandoraviruses show a distant relationship with other nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes, lack some of the NCLDV core genes and in particular do not appear to be specifically related to the other, better characterized family of giant viruses, the Mimiviridae. Here we report phylogenetic analysis of 6 core NCLDV genes that confidently places Pandoraviruses within the family Phycodnaviridae, with an apparent specific affinity with Coccolithoviruses. We conclude that, despite their many unusual characteristics, Pandoraviruses are highly derived phycodnaviruses. These findings imply that giant viruses have independently evolved from smaller NCLDV on at least two occasions.

Show MeSH
Related in: MedlinePlus