scholarly journals Isolation and Phylogenetic Analysis of Novel Viruses Infecting the Phytoplankton Phaeocystis globosa (Prymnesiophyceae)

2004 ◽  
Vol 70 (6) ◽  
pp. 3700-3705 ◽  
Author(s):  
C. P. D. Brussaard ◽  
S. M. Short ◽  
C. M. Frederickson ◽  
C. A. Suttle
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
Coastal Waters ◽  
Common Ancestor ◽  
Genetic Relatedness ◽  
Amino Acid Sequences ◽  
Polymerase Gene ◽  
Phaeocystis Globosa ◽  
The Family ◽  
Algal Host

ABSTRACT Viruses infecting the harmful bloom-causing alga Phaeocystis globosa (Prymnesiophyceae) were readily isolated from Dutch coastal waters (southern North Sea) in 2000 and 2001. Our data show a large increase in the abundance of putative P. globosa viruses during blooms of P. globosa, suggesting that viruses are an important source of mortality for this alga. In order to examine genetic relatedness among viruses infecting P. globosa and other phytoplankton, DNA polymerase gene (pol) fragments were amplified and the inferred amino acid sequences were phylogenetically analyzed. The results demonstrated that viruses infecting P. globosa formed a closely related monophyletic group within the family Phycodnaviridae, with at least 96.9% similarity to each other. The sequences grouped most closely with others from viruses that infect the prymnesiophyte algae Chrysochromulina brevifilum and Chrysochromulina strobilus. Whether the P. globosa viruses belong to the genus Prymnesiovirus or form a separate group needs further study. Our data suggest that, like their phytoplankton hosts, the Chrysochromulina and Phaeocystis viruses share a common ancestor and that these prymnesioviruses and their algal host have coevolved.

Phylogenetic analysis of PgV-102P, a new virus from the English Channel that infects Phaeocystis globosa

2006 ◽  
Vol 86 (3) ◽  
pp. 485-490 ◽  
Author(s):  
William H. Wilson ◽  
Declan C. Schroeder ◽  
Jenna Ho ◽  
Martin Canty
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
Harmful Algal Bloom ◽  
English Channel ◽  
Polymerase Gene ◽  
Phaeocystis Globosa ◽  
Dna Viruses ◽  
Algal Virus ◽  
Double Stranded Dna ◽  
Dna Polymerase Gene

A new virus that infects the harmful algal bloom-forming microalga Phaeocystis globosa was isolated from surface water in the English Channel off the coast of Plymouth, UK, in May 2001. Phylogenetic analysis of the DNA polymerase gene revealed the virus isolate, designated PgV-102P, belongs to the family Phycodnaviridae, a group of large double-stranded DNA viruses known to infect algae. Basic characterization of PgV-102P revealed it was a lytic virus with a relatively slow culture lysis period of 10-days. The genome size (176 kbp) and capsid diameter (98 nm) of PgV-102P fall at the bottom end of the range expected for phycodnaviruses. Interestingly, PgV-102P did not cluster with other P. globosa viruses; instead, it was more closely related to other prymnesioviruses that infect the marine prymnesiophyte Chrysochromulina brevifilum. We discuss the effectiveness of DNA polymerase as a diagnostic marker. Although it is ideal for determining what family or even genus an algal virus belongs to, it is clear that the DNA polymerase gene does not have sufficient resolution when looking for relationships within algal virus genera.

scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

Group II Nucleopolyhedrovirus Subgroups Revealed by Phylogenetic Analysis of Polyhedrin and DNA Polymerase Gene Sequences

1999 ◽  
Vol 73 (1) ◽  
pp. 59-73 ◽  
Author(s):  
Dieter M. Bulach ◽  
C.Ananth Kumar ◽  
Angelo Zaia ◽  
Bufeng Liang ◽  
David E. Tribe
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
Polymerase Gene ◽  
Gene Sequences ◽  
Dna Polymerase Gene ◽  
Group Ii

scholarly journals First Molecular Evidence for the Existence of Distinct Fish and Snake Adenoviruses

2002 ◽  
Vol 76 (19) ◽  
pp. 10056-10059 ◽  
Author(s):  
Mária Benkő ◽  
Péter Élő ◽  
Krisztina Ursu ◽  
Winfried Ahne ◽  
Scott E. LaPatra ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
New Genus ◽  
Molecular Evidence ◽  
Polymerase Gene ◽  
Snake Species ◽  
Dna Polymerase Gene

ABSTRACT From adenovirus-like viruses originating from a fish and a snake species, a conserved part of the adenoviral DNA polymerase gene was PCR amplified, cloned and sequenced. Phylogenetic analysis showed that the snake adenovirus is closely related to the members of the proposed genus Atadenovirus, whereas the fish isolate seems to represent a separate cluster, likely a new genus.

scholarly journals Duplication of a Truncated Paralog of the Family B DNA Polymerase Gene Aa-polB in the Agrocybe aegerita Mitochondrial Genome

2001 ◽  
Vol 67 (4) ◽  
pp. 1739-1743 ◽  
Author(s):  
Gerard Barroso ◽  
Frederic Bois ◽  
Jacques Labarère
Keyword(s):  
Mitochondrial Genome ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Polymerase Gene ◽  
Mitochondrial Trna ◽  
Amino Acid Similarity ◽  
Agrocybe Aegerita ◽  
Naturally Occurring ◽  
The Family ◽  
Dna Polymerase Gene

ABSTRACT The Agrocybe aegerita mitochondrial genome contains a truncated family B DNA polymerase gene (Aa-polB P1) whose nucleotide sequence is 86% identical to the previously described and potentially functional Aa-polB gene. A tRNAMetgene occurs at the 3′ end of the Aa-polB P1 gene. TheAa-polB P1 gene could result from reverse transcription of an Aa-polB mRNA primed by a tRNAMet followed by the integration of the cDNA after recombination at the mitochondrial tRNA locus. Two naturally occurring alleles of Aa-polB P1carry one or two copies of the disrupted sequence. In strains with two copies of Aa-polB P1, these copies are inverted relative to one another and separated by a short sequence carrying the tRNAMet gene. Both A. aegerita mitochondrial family B DNA polymerases were found to be related to other family B DNA polymerases (36 to 53% amino acid similarity), including the three enzymes of the archaebacterium Sulfolobus solfataricus. If mitochondria originated from a fusion between aClostridium-like eubacterium and aSulfolobus-like archaebacterium, then the A. aegerita family B DNA polymerase genes could be remnants of the archaebacterial genes.

scholarly journals Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene

2005 ◽  
Vol 86 (10) ◽  
pp. 2849-2858 ◽  
Author(s):  
H. Bourhy ◽  
J. A. Cowley ◽  
F. Larrous ◽  
E. C. Holmes ◽  
P. J. Walker
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Pcr Amplification ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Degenerate Primers ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Vector Borne

RNA viruses of the family Rhabdoviridae include arthropod-borne agents that infect plants, fish and mammals, and also include a variety of non-vector-borne mammalian viruses. Herein is presented a molecular phylogenetic analysis, the largest undertaken to date, of 56 rhabdoviruses, including 20 viruses which are currently unassigned or assigned as tentative species within the Rhabdoviridae. Degenerate primers targeting a region of block III of the L polymerase gene were defined and used for RT-PCR amplification and sequencing. A maximum-likelihood phylogenetic analysis of a 158-residue L polymerase amino acid sequence produced an evolutionary tree containing the six recognized genera of the Rhabdoviridae and also enabled us to identify four more monophyletic groups of currently unclassified rhabdoviruses that we refer to as the ‘Hart Park’, ‘Almpiwar’, ‘Le Dantec’ and ‘Tibrogargan’ groups. The broad phylogenetic relationships among these groups and genera also indicate that the evolutionary history of rhabdoviruses was strongly influenced by mode of transmission, host species (plant, fish or mammal) and vector (orthopteran, homopteran or dipteran).

Phylogenetic Analysis of the DNA Polymerase Gene of a Novel Alphaherpesvirus Isolated from an Indian Gyps Vulture

Virus Genes ◽  
2005 ◽  
Vol 30 (3) ◽  
pp. 371-381 ◽  
Author(s):  
Maria Cardoso ◽  
Alex Hyatt ◽  
Paul Selleck ◽  
Sue Lowther ◽  
Vibhu Prakash ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
Polymerase Gene ◽  
Dna Polymerase Gene

scholarly journals Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

2019 ◽  
Vol 165 (1) ◽  
pp. 21-31 ◽  
Author(s):  
A. M. Dullemans ◽  
M. Botermans ◽  
M. J. D. de Kock ◽  
C. E. de Krom ◽  
T. A. J. van der Lee ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Complete Genome ◽  
New Genus ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Ringspot Virus ◽  
Genome Sequences ◽  
The Family ◽  
Virus Isolates

Abstract To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

scholarly journals Integrating Reptilian Herpesviruses into the Family Herpesviridae

2005 ◽  
Vol 79 (2) ◽  
pp. 725-731 ◽  
Author(s):  
Duncan J. McGeoch ◽  
Derek Gatherer
Keyword(s):  
Amino Acid ◽  
Dna Polymerase ◽  
Bayesian Methods ◽  
Protein Sequences ◽  
Dna Binding Protein ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
New Members ◽  
The Family ◽  
Branching Patterns

ABSTRACT The phylogeny of reptilian herpesviruses (HVs) relative to mammalian and avian HVs was investigated by using available gene sequences and by alignment of encoded amino acid sequences and derivation of trees by maximum-likelihood and Bayesian methods. Phylogenetic loci were obtained for green turtle HV (GTHV) primarily on the basis of DNA polymerase (POL) and DNA binding protein sequences, and for lung-eye-trachea disease-associated HV (LETV) primarily from its glycoprotein B sequence; both have nodes on the branch leading to recognized species in the Alphaherpesvirinae subfamily and should be regarded as new members of that subfamily. A similar but less well defined locus was obtained for an iguanid HV based on a partial POL sequence. On the basis of short POL sequences (around 60 amino acid residues), it appeared likely that GTHV and LETV belong to a private clade and that three HVs of gerrhosaurs (plated lizards) are associated with the iguanid HV. Based on phylogenetic branching patterns for mammalian HV lineages that mirror those of host lineages, we estimated a date for the HV tree's root of around 400 million years ago. Estimated dates for branching events in the development of reptilian, avian, and mammalian Alphaherpesvirinae lineages could plausibly be accounted for in part but not completely by ancient coevolution of these virus lines with reptilian lineages and with the development of birds and mammals from reptilian progenitors.

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