Comparative genomic analysis of the family Iridoviridae : re-annotating and defining the core set of iridovirus genes
TLDR
The re-analysis of genomes within the Iridoviridae family provides a unifying framework to understand the biology of these viruses, and further re-defining the core set of iridovirus genes will continue to lead to a better understanding of the phylogenetic relationships between individual irids.Abstract:
Members of the family Iridoviridae can cause severe diseases resulting in significant economic and environmental losses. Very little is known about how iridoviruses cause disease in their host. In the present study, we describe the re-analysis of the Iridoviridae family of complex DNA viruses using a variety of comparative genomic tools to yield a greater consensus among the annotated sequences of its members. A series of genomic sequence comparisons were made among, and between the Ranavirus and Megalocytivirus genera in order to identify novel conserved ORFs. Of these two genera, the Megalocytivirus genomes required the greatest number of altered annotations. Prior to our re-analysis, the Megalocytivirus species orange-spotted grouper iridovirus and rock bream iridovirus shared 99% sequence identity, but only 82 out of 118 potential ORFs were annotated; in contrast, we predict that these species share an identical complement of genes. These annotation changes allowed the redefinition of the group of core genes shared by all iridoviruses. Seven new core genes were identified, bringing the total number to 26. Our re-analysis of genomes within the Iridoviridae family provides a unifying framework to understand the biology of these viruses. Further re-defining the core set of iridovirus genes will continue to lead us to a better understanding of the phylogenetic relationships between individual iridoviruses as well as giving us a much deeper understanding of iridovirus replication. In addition, this analysis will provide a better framework for characterizing and annotating currently unclassified iridoviruses.read more
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Viral Serine/Threonine Protein Kinases
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Nicola Segata,Curtis Huttenhower +1 more
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Concurrence of Iridovirus, Polyomavirus, and a Unique Member of a New Group of Fish Papillomaviruses in Lymphocystis Disease-Affected Gilthead Sea Bream.
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Characterization of a megalocytivirus from cultured rock bream, Oplegnathus fasciatus (Temminck & Schlege), in China
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A Novel Virus Causes Scale Drop Disease in Lates calcarifer
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TL;DR: Findings show that the virus is the causative agent for the scale drop syndrome, as each of Koch’s postulates is fulfilled.
References
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Journal ArticleDOI
Emerging infectious diseases and amphibian population declines.
TL;DR: The role of these diseases in the global decline of amphibian populations is examined and hypotheses for the origins and impact of these panzootics are proposed.
Journal ArticleDOI
Infectious disease and amphibian population declines
TL;DR: It is suggested that, in common with many emerging infectious diseases of humans, domestic animals and other wildlife species, emergence of chytridiomycosis may be driven by anthropogenic introduction (pathogen pollution).
Journal ArticleDOI
Measuring genome evolution.
Martijn A. Huynen,Peer Bork +1 more
TL;DR: A hierarchy of rates at which genomes have changed during evolution is established and it is shown that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.
Journal ArticleDOI
Complete genome analysis of the mandarin fish infectious spleen and kidney necrosis iridovirus.
TL;DR: It is suggested that ISKNV, RSIV, sea bass iridovirus, grouper iridvirus, and African lampeye iridavirus may belong to a new genus of the Iridoviridae family and are tentatively referred to as cell hypertrophy iridOViruses.