Comparative genomic analysis of the family Iridoviridae : re-annotating and defining the core set of iridovirus genes
Citations
292 citations
Cites background from "Comparative genomic analysis of the..."
...Smithsonian Institute, Washington, DC, p 127–136 Chinchar VG (2002) Ranaviruses (family Iridoviridae): emerging cold-blooded killers....
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...However, electron microscopy is only reliable for identification to the family level (Iridoviridae); it cannot be used to definitively verify a ranavirus....
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...Ranavirus is in the family Iridoviridae (Eaton et al. 2007), which contains 5 genera: 2 infect invertebrates (Iridovirus and Chloriridovirus) and 3 infect ectothermic vertebrates (Ranavirus, Megalocytivirus, and Lymphocystivirus; Chinchar et al. 2009)....
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...Virology 306:303–312 Chinchar VG, Essbauer S, He JG, Hyatt A, Miyazaki T, Seligy V, Williams T (2005) Iridoviridae....
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...Ecol Lett 9:1157–1171 Ridenhour BJ, Storfer AT (2008) Geographically variable selection in Ambystoma tigrinum virus (Iridoviridae) throughout the western USA....
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219 citations
Cites background or methods from "Comparative genomic analysis of the..."
...…of the two largest subunits of host Pol II (designated vPol-IIα and -IIβ) in all iridovirids sequenced to date strongly suggests that late in infection viral transcription is catalyzed by a virus-modified, or virusencoded, DNA-dependent RNA polymerase (Williams et al. 2005; Eaton et al. 2007)....
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...Overall, iridovirids contain a common set of viral genes that encode viral structural and catalytic proteins that permit replication in a broad range of cell types (Eaton et al. 2007)....
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...The numbers shown are averages based on the estimates of Eaton et al. (2007) and Tsai et al. (2007) b11951193-0004ztc.indd 128 8/18/2008 5:51:38 PM...
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...Although there is still some disagreement on the exact numbers, based on the genome size, iridovirids contain between roughly 100 (ATV and FV3) and 200 (IIV-6) open reading frames (ORFs) (Tsai et al. 2007; Eaton et al. 2007; see Table 2 )....
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...Most of the remaining ORFs match putative proteins present in one or more iridovirids, suggesting that they play important roles in iridovirid replication, biogenesis, and survival (Eaton et al. 2007)....
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Cites background or methods from "Comparative genomic analysis of the..."
...(34) was used to analyze read density per ORF....
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...The IIV-6 genome is predicted to encode 211 ORFs, of which 45% and 55% derive from the upper and lower strands, respectively (34)....
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...IIV-6 is a large, complex virus with a dsDNA genome of 212,482 bp that encodes 211 putative ORFs distributed along the two strands of the viral genome (33, 34)....
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References
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779 citations
"Comparative genomic analysis of the..." refers background in this paper
...In addition, iridovirus infections have been implicated in amphibian population declines, representing a set of emerging infectious diseases whose spread has been accelerated by human activities [10-14]....
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442 citations
"Comparative genomic analysis of the..." refers background in this paper
...The first step in the re-annotation of the Ranavirus genus was a comparative genomic analysis of FV3, TFV, and ATV....
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...Results: A series of genomic sequence comparisons were made among, and between the Ranavirus and Megalocytivirus genera in order to identify novel conserved ORFs....
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...Subsequent reanalysis of the second Ranavirus group, containing SGIV and GIV, resulted in an increase from 131 to 138 conserved annotated ORFs (Table 4)....
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...After re-annotating the Megalocytivirus genus, we applied the same comparative genomic analysis to the Ranavirus genus....
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...Although this approach proved extremely successful for the Ranavirus and Megalocytivirus genera, we were unable to use it for the Chloriridovirus, Iridovirus, and Lymphocystivirus genera....
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437 citations
"Comparative genomic analysis of the..." refers background in this paper
...This type of analysis is rarely consistent due to horizontal gene transfer [28] and variable rates of evolution [29]....
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235 citations
"Comparative genomic analysis of the..." refers background in this paper
...Frog virus 3 FV3 Ranavirus 105903 97 AY548484 [27] Tiger frog virus TFV Ranavirus 105057 103 AF389451 [1] Ambystoma tigrinum virus ATV Ranavirus 106332 92 AY150217 [30] Grouper iridovirus GIV Ranavirus 139793 139 AY666015 [21] Singapore grouper iridovirus SGIV Ranavirus 140131 139 AY521625 [22] Lymphocystis disease virus 1 LCDV-1 Lymphocystivirus 102653 108 L63545 [34] Lymphocystis disease virus China LCDV-China Lymphocystivirus 186250 178 AY380826 [24] Infectious spleen and kidney necrosis virus ISKNV Megalocytivirus 111362 117 AF371960 [20] Rock bream iridovirus RBIV Megalocytivirus 112080 116 AY532606 [19] Orange-spotted grouper iridovirus OSGIV Megalocytivirus 112636 116 AY894343 [18] Invertebrate iridescent virus 6 IIV-6 Iridovirus 212482 211 AF303741 [2] Invertebrate iridescent virus 3 IIV-3 Chloriridovirus 191100 126 DQ643392 [26]...
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...A number of past phylogenetic analyses of Iridoviridae have used phylogenic trees constructed from aligned protein sequences [1,18-20,22,24,27]....
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...It is interesting to note that the genomic sequence of ISKNV (sequenced using subcloned fragments rather than PCR products) [20], had significantly fewer annotation changes made during our re-analysis....
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