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      A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

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          Abstract

          The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus ( Nudiviridae).

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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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            The Oryctes virus: its detection, identification, and implementation in biological control of the coconut palm rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae).

            In view of the increasing and devastating damage by rhinoceros beetle (Oryctes rhinoceros) to coconut palms in the middle of last century, many efforts were made to find an efficient natural control factor against this pest, which could not be controlled by pesticides. The basic procedures of these monitoring programmes are outlined together with the final detection of a virus disease in oil palm estates in Malaysia in 1963. In extensive laboratory studies, the virus was isolated and identified as the first non-occluded, rod-shaped insect virus, morphologically resembling the baculoviruses. Infection experiments clarified the pathology, histopathology, and virulence of the virus and demonstrated that the virus was extremely virulent to larvae after peroral application. These findings encouraged the first pilot release of virus in 1967 in coconut plantations of Western Samoa where breeding sites were contaminated with virus. Surprisingly, the virus became established in the Samoan rhinoceros beetle populations and spread autonomously throughout the Western Samoan islands. As a consequence, there was a drastic decline of the beetle populations followed by a conspicuous recovery of the badly damaged coconut stands. This unexpected phenomenon could only be explained after it was shown that the adult beetle itself is a very active virus vector and thus was responsible for the efficient autodissemination of the virus. The functioning of the beetle as a 'flying virus factory' is due to the unique cytopathic process developing in the midgut after peroral virus infection. Pathological details of this process are presented. Because of the long-term persistence of the virus in the populations, rhinoceros beetle control is maintained. Incorporation of virus into integrated control measures and successful virus releases in many other countries are recorded.
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              Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2014).

              Changes to virus taxonomy approved by a vote of all ICTV members in February-March 2014 are reported.
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                Author and article information

                Contributors
                J.Bojko@tees.ac.uk
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                9 September 2020
                9 September 2020
                2020
                : 10
                : 14816
                Affiliations
                [1 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, School of Forest Resource and Conservation, , University of Florida, ; Gainesville, FL 32611 USA
                [2 ]GRID grid.14332.37, ISNI 0000 0001 0746 0155, International Centre of Excellence for Aquatic Animal Health, Centre for Environment, , Fisheries and Aquatic Science (Cefas), ; Weymouth, Dorset, DT4 8UB UK
                [3 ]GRID grid.8391.3, ISNI 0000 0004 1936 8024, Centre for Sustainable Aquaculture Futures, Biosciences, , University of Exeter, ; Stocker Road, Exeter, EX4 4PY UK
                [4 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, Fisheries and Aquatic Sciences, , University of Florida, ; Gainesville, FL 32653 USA
                [5 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, Emerging Pathogens Institute, , University of Florida, ; Gainesville, FL 32611 USA
                [6 ]GRID grid.26597.3f, ISNI 0000 0001 2325 1783, School of Health and Life Science, , Teesside University, ; Middlesbrough, TS1 3BA UK
                [7 ]GRID grid.26597.3f, ISNI 0000 0001 2325 1783, National Horizons Centre of Excellence in Bioscience Industry, , Teesside University, ; Darlington, DL1 1HG UK
                Article
                71776
                10.1038/s41598-020-71776-3
                7481228
                186a5bc1-42ec-496c-9ad2-c02a5f45f94c
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 February 2020
                : 4 August 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100012534, Centre for Environment, Fisheries and Aquaculture Science;
                Award ID: FB002
                Funded by: FundRef http://dx.doi.org/10.13039/501100000270, Natural Environment Research Council;
                Award ID: 1368300
                Award Recipient :
                Categories
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                © The Author(s) 2020

                Uncategorized
                ecology,virology
                Uncategorized
                ecology, virology

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