Phylogenetic Analysis of Members of the
            <i>Phycodnaviridae</i>
            Virus Family, Using Amplified Fragments of the Major Capsid Protein Gene

Larsen, Jens Borggaard; Larsen, Aud; Bratbak, Gunnar; Sandaa, Ruth Anne

doi:10.1128/aem.02548-07

Cited by 91 publications

(113 citation statements)

References 52 publications

(50 reference statements)

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“…These results are consistent with those from previous studies demonstrating that all, or nearly all environmental sequences obtained with the AVS-1 and 2 primers cluster with polB genes from marine prasinoviruses (for example, Short and Suttle, 2002;Short and Short, 2008;Clasen and Suttle, 2009;Culley et al, 2009). It is known that these primers do not amplify polB genes from other phycodnaviruses, such as Emiliania huxleyi virus, Heterosigma akashiwo virus, Chrysochromulina ericina virus and Pyramimonas orientalis virus, for example, Larsen et al, 2008). Thus, it is apparent that the AVS primers amplify only a subset of phycodnaviruses and might even be biased for prasinoviruses.…”

Section: Resultssupporting

confidence: 82%

“…The earliest effort to characterize phycodnavirus communities while circumventing difficulties associated with virus cultivation involved designing algal-virus specific (AVS) PCR primers that targeted DNA polymerase (polB) genes . Clone libraries of polB amplicons, and more recently amplicons of a gene encoding the major capsid protein (Larsen et al, 2008), demonstrated that phycodnavirus communities are diverse, environmental sequences are distinct from cultivated phycodnavirus genes, and closely related sequences can be found in geographically distant locations (Short and Suttle, 2002;Larsen et al, 2008;Short and Short, 2008;Clasen and Suttle, 2009). Although studies of phycodnavirus diversity have provided many insights into their ecology, they do not yield quantitative information to infer their influence on phytoplankton mortality and succession, or the flow of energy and material in aquatic systems.…”

Section: Introductionmentioning

confidence: 99%

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Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

2010

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Using quantitative PCR, the abundances of six phytoplankton viruses DNA polymerase (polB) gene fragments were estimated in water samples collected from Lake Ontario, Canada over 26 months. Four of the polB fragments were most related to marine prasinoviruses, while the other two were most closely related to cultivated chloroviruses. Two Prasinovirus-related genes reached peak abundances of 41000 copies ml À1 and were considered 'high abundance', whereas the other two Prasinovirus-related genes peaked at abundances o1000 copies ml À1 and were considered 'low abundance'. Of the genes related to chloroviruses, one peaked at ca 1600 copies ml À1 , whereas the other reached only ca 300 copies ml À1 . Despite these differences in peak abundance, the abundances of all genes monitored were lowest during the late fall, winter and early spring; during these months the high abundance genes persisted at 100-1000 copies ml À1 while the low abundance Prasinovirus-and Chlorovirus-related genes persisted at fewer than ca 100 copies ml À1 . Clone libraries of psbA genes from Lake Ontario revealed numerous Chlorella-like algae and two prasinophytes demonstrating the presence of candidate hosts for all types of viruses monitored. Our results corroborate recent metagenomic analyses that suggest that aquatic virus communities are composed of only a few abundant populations and many low abundance populations. Thus, we speculate that an ecologically important characteristic of phycodnavirus communities is seed-bank populations with members that can become numerically dominant when their host abundances reach appropriate levels.

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Section: Resultssupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

2010

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“…Inteins appear to be most common in Archaea, but have been identified in all three domains of life and in viruses (Perler, 2002). Among the phycodnaviruses, inteins have been identified in the DNA polymerase I of H. akashiwo virus (HaV; Nagasaki et al, 2005) and Chrysochromulina ercina virus (CeV; Larsen et al, 2008) and in the helicase and ribonucleotide reductase of the PBCV (NY-2A; Fitzgerald et al, 2007). Little is known about the prevalence or diversity of inteins among the large number of marine phycodnaviruses that have not been cultivated.…”

Section: Introductionmentioning

confidence: 99%

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

2008

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Viruses in the family Phycodnaviridae infect autotrophic protists in aquatic environments. Application of a PCR assay targeting the DNA polymerase of viruses in this family has revealed that phycodnaviruses are quite diverse and appear to be widespread, but a limited number of environments have been examined so far. In this study, we examined the sequence diversity among viral DNA pol genes amplified by PCR from subtropical coastal waters of O'ahu, Hawai'i. A total of 18 novel prasinovirus-like sequences were detected along with two other divergent sequences that differ at the genus-level relative to other sequences in the family. Of the 20 new sequence types reported here, three were serendipitously found to contain protein introns, or inteins. Sequence analysis of the inteins suggested that all three have self-splicing domains and are apparently capable of removing themselves from the translated polymerase protein. Two of the three also appear to be 'active', meaning they encode all the motifs necessary for a complete dodecapeptide homing endonuclease, and are therefore capable of horizontal transfer. A subsequent PCR survey of our samples with intein-specific primers suggested that intein-containing phycodnaviruses are common in this environment. A search for similar sequences in metagenomic data sets from other oceans indicated that viral inteins are also widespread, but how these genetic parasites might be influencing the ecology and evolution of phycodnaviruses remains unclear.

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“…Remarkably, these viruses exhibit the two largest known genomes among marine viruses: 730 kb and 1.28 Mb for CroV and Megavirus chilensis, respectively. Other studies, targeting virus-specific genes [e.g., DNA polymerase B (8) or capsid proteins (9)] have suggested a close phylogenetic relationship between Mimivirus and several giant dsDNA viruses infecting various unicellular algae such as Pyramimonas orientalis (Chlorophyta, Prasinophyceae), Phaeocystis pouchetii (Haptophyta, Prymnesiophyceae), and Chrysochromulina ericina (Haptophyta, Prymnesiophyceae).…”

mentioning

confidence: 99%

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Santini

Jeudy

Bartoli

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

166

194

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Large dsDNA viruses are involved in the population control of many globally distributed species of eukaryotic phytoplankton and have a prominent role in bloom termination. The genus Phaeocystis ( Haptophyta , Prymnesiophyceae ) includes several high-biomass-forming phytoplankton species, such as Phaeocystis globosa , the blooms of which occur mostly in the coastal zone of the North Atlantic and the North Sea. Here, we report the 459,984-bp-long genome sequence of P. globosa virus strain PgV-16T, encoding 434 proteins and eight tRNAs and, thus, the largest fully sequenced genome to date among viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic affinity with other viruses infecting microalgae (e.g., phycodnaviruses), including those infecting Emiliania huxleyi , another ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to an emerging clade (the Megaviridae) clustering the viruses endowed with the largest known genomes, including Megavirus, Mimivirus (both infecting acanthamoeba), and a virus infecting the marine microflagellate grazer Cafeteria roenbergensis . Seventy-five percent of the best matches of PgV-16T–predicted proteins correspond to two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from a hypersaline lake in Antarctica (Organic Lake), the hosts of which are unknown. As for OLPVs and other Megaviridae, the PgV-16T sequence data revealed the presence of a virophage-like genome. However, no virophage particle was detected in infected P. globosa cultures. The presence of many genes found only in Megaviridae in its genome and the presence of an associated virophage strongly suggest that PgV-16T shares a common ancestry with the largest known dsDNA viruses, the host range of which already encompasses the earliest diverging branches of domain Eukarya.

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Phylogenetic Analysis of Members of the Phycodnaviridae Virus Family, Using Amplified Fragments of the Major Capsid Protein Gene

Cited by 91 publications

References 52 publications

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

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