Detection of diverse marine algal viruses in the South Sea regions of Korea by PCR amplification of the DNA polymerase and major capsid protein genes

2011 ◽  
Vol 159 (1) ◽  
pp. 43-50 ◽  
Author(s):  
Yunjung Park ◽  
Kyungyong Lee ◽  
Yong Seok Lee ◽  
Si Wouk Kim ◽  
Tae-Jin Choi
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
Major Capsid Protein ◽  
Pcr Amplification ◽  
The South ◽  
Algal Viruses ◽  
South Sea ◽  
Marine Algal

scholarly journals Ranavirus phylogeny and differentiation based on major capsid protein, DNA polymerase and neurofilament triplet H1-like protein genes

2009 ◽  
Vol 85 ◽  
pp. 81-91 ◽  
Author(s):  
R Holopainen ◽  
S Ohlemeyer ◽  
H Schütze ◽  
SM Bergmann ◽  
H Tapiovaara
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
Major Capsid Protein

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

2008 ◽  
Vol 74 (10) ◽  
pp. 3048-3057 ◽  
Author(s):  
J. B. Larsen ◽  
A. Larsen ◽  
G. Bratbak ◽  
R.-A. Sandaa
Keyword(s):  
Phylogenetic Analysis ◽  
Capsid Protein ◽  
Major Capsid Protein ◽  
Pcr Primers ◽  
Type I ◽  
Virus Family ◽  
The Family ◽  
Algal Viruses ◽  
Viral Communities ◽  
Phaeocystis Pouchetii

ABSTRACT Algal viruses are considered ecologically important by affecting host population dynamics and nutrient flow in aquatic food webs. Members of the family Phycodnaviridae are also interesting due to their extraordinary genome size. Few algal viruses in the Phycodnaviridae family have been sequenced, and those that have been have few genes in common and low gene homology. It has hence been difficult to design general PCR primers that allow further studies of their ecology and diversity. In this study, we screened the nine type I core genes of the nucleocytoplasmic large DNA viruses for sequences suitable for designing a general set of primers. Sequence comparison between members of the Phycodnaviridae family, including three partly sequenced viruses infecting the prymnesiophyte Pyramimonas orientalis and the haptophytes Phaeocystis pouchetii and Chrysochromulina ericina (Pyramimonas orientalis virus 01B [PoV-01B], Phaeocystis pouchetii virus 01 [PpV-01], and Chrysochromulina ericina virus 01B [CeV-01B], respectively), revealed eight conserved regions in the major capsid protein (MCP). Two of these regions also showed conservation at the nucleotide level, and this allowed us to design degenerate PCR primers. The primers produced 347- to 518-bp amplicons when applied to lysates from algal viruses kept in culture and from natural viral communities. The aim of this work was to use the MCP as a proxy to infer phylogenetic relationships and genetic diversity among members of the Phycodnaviridae family and to determine the occurrence and diversity of this gene in natural viral communities. The results support the current legitimate genera in the Phycodnaviridae based on alga host species. However, while placing the mimivirus in close proximity to the type species, PBCV-1, of Phycodnaviridae along with the three new viruses assigned to the family (PoV-01B, PpV-01, and CeV-01B), the results also indicate that the coccolithoviruses and phaeoviruses are more diverged from this group. Phylogenetic analysis of amplicons from virus assemblages from Norwegian coastal waters as well as from isolated algal viruses revealed a cluster of viruses infecting members of the prymnesiophyte and prasinophyte alga divisions. Other distinct clusters were also identified, containing amplicons from this study as well as sequences retrieved from the Sargasso Sea metagenome. This shows that closely related sequences of this family are present at geographically distant locations within the marine environment.

scholarly journals Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water

2019 ◽  
Vol 93 (8) ◽  
Author(s):  
Genki Yoshikawa ◽  
Romain Blanc-Mathieu ◽  
Chihong Song ◽  
Yoko Kayama ◽  
Tomohiro Mochizuki ◽  
...  
Keyword(s):  
Dna Replication ◽  
Capsid Protein ◽  
Dna Polymerase ◽  
Major Capsid Protein ◽  
Hot Spring ◽  
Morphological Characteristics ◽  
Spring Water ◽  
Dna Virus ◽  
Dna Viruses ◽  
Content Type

ABSTRACT Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae. IMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.

scholarly journals Promoter analysis of the Chilo iridescent virus DNA polymerase and major capsid protein genes

Virology ◽  
2003 ◽  
Vol 317 (2) ◽  
pp. 321-329 ◽  
Author(s):  
Remziye Nalçacioğlu ◽  
Hendrik Marks ◽  
Just M. Vlak ◽  
Zihni Demirbaĝ ◽  
Monique M. van Oers
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
Promoter Analysis ◽  
Major Capsid Protein ◽  
Chilo Iridescent Virus ◽  
Iridescent Virus

scholarly journals Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes

2014 ◽  
Vol 80 (10) ◽  
pp. 3150-3160 ◽  
Author(s):  
Camille Clerissi ◽  
Nigel Grimsley ◽  
Hiroyuki Ogata ◽  
Pascal Hingamp ◽  
Julie Poulain ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
High Throughput Sequencing ◽  
Major Capsid Protein ◽  
Content Type ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Genes Encoding ◽  
Conserved Genes ◽  
Primer Sets

ABSTRACTViruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present inPrasinovirusgenomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage ofPrasinovirusdiversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.

scholarly journals Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

2014 ◽  
Vol 8 (10) ◽  
pp. 2093-2103 ◽  
Author(s):  
Max Hopkins ◽  
Shweta Kailasan ◽  
Allison Cohen ◽  
Simon Roux ◽  
Kimberly Pause Tucker ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Major Capsid Protein ◽  
Pcr Amplification ◽  
Single Stranded Dna
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