Complete Genome Sequence of a Bohle iridovirus Isolate from Ornate Burrowing Frogs (Limnodynastes ornatus) in Australia

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Abstract

Bohle iridovirus (BIV) is a species within the genus Ranavirus, family Iridoviridae, first isolated from the ornate burrowing frog Limnodynastes ornatus in Australia. The BIV genome confirms it is closely related to isolates from boreal toad Anaxyrus boreas and leaf-tailed gecko Uroplatus fimbriatus within the United States and Germany, respectively.

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Most cited references 11

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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

Heather Eaton, Julie Metcalf, Emily Penny … (2007)

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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Phylogeny and Differentiation of Reptilian and Amphibian Ranaviruses Detected in Europe

Anke C. Stöhr, Alberto López-Bueno, Silvia Blahak … (2015)

Ranaviruses in amphibians and fish are considered emerging pathogens and several isolates have been extensively characterized in different studies. Ranaviruses have also been detected in reptiles with increasing frequency, but the role of reptilian hosts is still unclear and only limited sequence data has been provided. In this study, we characterized a number of ranaviruses detected in wild and captive animals in Europe based on sequence data from six genomic regions (major capsid protein (MCP), DNA polymerase (DNApol), ribonucleoside diphosphate reductase alpha and beta subunit-like proteins (RNR-α and -β), viral homolog of the alpha subunit of eukaryotic initiation factor 2, eIF-2α (vIF-2α) genes and microsatellite region). A total of ten different isolates from reptiles (tortoises, lizards, and a snake) and four ranaviruses from amphibians (anurans, urodeles) were included in the study. Furthermore, the complete genome sequences of three reptilian isolates were determined and a new PCR for rapid classification of the different variants of the genomic arrangement was developed. All ranaviruses showed slight variations on the partial nucleotide sequences from the different genomic regions (92.6–100%). Some very similar isolates could be distinguished by the size of the band from the microsatellite region. Three of the lizard isolates had a truncated vIF-2α gene; the other ranaviruses had full-length genes. In the phylogenetic analyses of concatenated sequences from different genes (3223 nt/10287 aa), the reptilian ranaviruses were often more closely related to amphibian ranaviruses than to each other, and most clustered together with previously detected ranaviruses from the same geographic region of origin. Comparative analyses show that among the closely related amphibian-like ranaviruses (ALRVs) described to date, three recently split and independently evolving distinct genetic groups can be distinguished. These findings underline the wide host range of ranaviruses and the emergence of pathogen pollution via animal trade of ectothermic vertebrates.

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Author and article information

Journal

Journal ID (nlm-ta): Genome Announc

Journal ID (iso-abbrev): Genome Announc

Journal ID (hwp): ga

Journal ID (pmc): ga

Journal ID (publisher-id): GA

Title: Genome Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2169-8287

Publication date (Electronic): 18 August 2016

Publication date Collection: Jul-Aug 2016

Volume: 4

Issue: 4

Electronic Location Identifier: e00632-16

Affiliations

[a ]OIE Reference Laboratory for Epizootic Hematopoietic Necrosis Virus and Ranavirus Infection of Amphibians, Faculty of Veterinary Science, School of Life and Environment Sciences, The University of Sydney, Sydney, Australia

[b ]Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

Author notes

Address correspondence to Paul M. Hick, paul.hick@ 123456sydney.edu.au .

This article is dedicated to Rick Speare.

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Kuttichantran Subramaniam http://orcid.org/0000-0002-2752-4467

Article

Publisher ID: genomeA00632-16

DOI: 10.1128/genomeA.00632-16

PMC ID: 4991696

PubMed ID: 27540051

SO-VID: 73a5f5af-1d26-44f7-8a61-245c84501c6d

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

History

Date received : 14 May 2016

Date accepted : 23 June 2016

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Figures: 0, Tables: 0, Equations: 0, References: 18, Pages: 2, Words: 1381

Funding

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

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cover-date July/August 2016

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ScienceOpen disciplines: Genetics

Complete Genome Sequence of a Bohle iridovirus Isolate from Ornate Burrowing Frogs ( Limnodynastes ornatus) in Australia

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Most cited references 11

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

Comparative genomic analysis of the family Iridoviridae: re-annotating and defining the core set of iridovirus genes

Phylogeny and Differentiation of Reptilian and Amphibian Ranaviruses Detected in Europe

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