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      Genomic Sequencing of Ranaviruses Isolated from Turbot ( Scophthalmus maximus) and Atlantic Cod ( Gadus morhua)

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          Abstract

          Ranaviruses have been isolated from Atlantic cod ( Gadus morhua) and turbot ( Scophthalmus maximus) in Denmark. Phylogenomic analyses revealed that these two ranaviruses are nearly identical and form a distinct clade at the base of the ranavirus tree branching off near other fish ranaviruses.

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          GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

          J Besemer (2001)
          Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely 83.2% of the translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts in an experimentally validated set of Escherichia coli genes. We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection methods. Accurate translation start prediction, in addition to the refinement of protein sequence N-terminal data, provides the benefit of precise positioning of the sequence region situated upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites can be revealed and analyzed with higher precision. These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed.
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            Comparative genomic analysis of the family Iridoviridae: re-annotating and defining the core set of iridovirus genes

            Background 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. Results 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. Conclusion 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.
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              Comparative study of ranavirus isolates from cod (Gadus morhua) and turbot (Psetta maxima) with reference to other ranaviruses.

              Two iridovirus isolates recovered from cod (Gadus morhua) and turbot (Psetta maxima) in Denmark were examined in parallel with a panel of other ranaviruses including frog virus 3 (FV3), the reference strain for the genus Ranavirus. The isolates were assessed according to their reactivity in immunofluoresent antibody tests (IFAT) using both homologous and heterologous antisera and their amplification in PCR using primers targeting five genomic regions. The corresponding PCR fragments were sequenced, and the sequences obtained were used in phylogenetic analysis. In addition, the pathogenicity to rainbow trout under experimental challenge conditions was investigated. The viruses were serologically and genetically closely related to highly pathogenic ranaviruses such as European catfish iridovirus (ECV), European sheatfish iridovirus (ESV) and epizootic haematopoietic necrosis virus (EHNV). The challenge trials indicate that rainbow trout fry cultured at 15 degrees C are not target species for the virus isolates in the present panel. We suggest that the two isolates belong in the genus Ranavirus and propose the name Ranavirus maxima (Rmax) for the turbot isolate.
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                Author and article information

                Journal
                Genome Announc
                Genome Announc
                ga
                ga
                GA
                Genome Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2169-8287
                15 December 2016
                Nov-Dec 2016
                : 4
                : 6
                : e01393-16
                Affiliations
                [a ]College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
                [b ]Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
                [c ]Technical University of Denmark, National Veterinary Institute, Frederiksberg C, Denmark
                Author notes
                Address correspondence to Ellen Ariel, ellen.ariel@ 123456jcu.edu.au .
                Author information
                http://orcid.org/0000-0002-2752-4467
                Article
                genomeA01393-16
                10.1128/genomeA.01393-16
                5159577
                27979944
                65c0f8b8-eb0c-4f84-bf07-c7a2e29f4707
                Copyright © 2016 Ariel et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 19 October 2016
                : 21 October 2016
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 11, Pages: 2, Words: 1164
                Funding
                This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
                Categories
                Viruses
                Custom metadata
                November/December 2016

                Genetics
                Genetics

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