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      Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans

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          Abstract

          Background

          The White Spot Syndrome Virus (WSSV) is an important pathogen that infects a variety of decapod species and causes a highly contagious disease in penaeid shrimps. Mass mortalities caused by WSSV have pronounced commercial impact on shrimp aquaculture. Until now WSSV is the only known member of the virus family Nimaviridae, a group with obscure phylogenetic affinities. Its isolated position makes WSSV studies challenging due to large number of genes without homology in other viruses or cellular organisms.

          Results

          Here we report the discovery of an unusually large amount of sequences with high similarity to WSSV in a genomic library from the Jamaican bromeliad crab Metopaulias depressus. De novo assembly of these sequences allowed for the partial reconstruction of the genome of this endogenized virus with total length of 200 kbp encompassed in three scaffolds. The genome includes at least 68 putative open reading frames with homology in WSSV, most of which are intact. Among these, twelve orthologs of WSSV genes coding for non-structural proteins and nine genes known to code for the major components of the WSSV virion were discovered. Together with reanalysis of two similar cases of WSSV-like sequences in penaeid shrimp genomic libraries, our data allowed comparison of gene composition and gene order between different lineages related to WSSV. Furthermore, screening of published sequence databases revealed sequences with highest similarity to WSSV and the newly described virus in genomic libraries of at least three further decapod species. Analysis of the viral sequences detected in decapods suggests that they are less a result of contemporary WSSV infection, but rather originate from ancestral infection events. Phylogenetic analyses suggest that genes were acquired repeatedly by divergent viruses or viral strains of the Nimaviridae.

          Conclusions

          Our results shed new light on the evolution of the Nimaviridae and point to a long association of this viral group with decapod crustaceans.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12862-015-0380-7) contains supplementary material, which is available to authorized users.

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          Most cited references39

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          Finely orchestrated movements: evolution of the ribosomal RNA genes.

          Evolution of the tandemly repeated ribosomal RNA (rRNA) genes is intriguing because in each species all units within the array are highly uniform in sequence but that sequence differs between species. In this review we summarize the origins of the current models to explain this process of concerted evolution, emphasizing early studies of recombination in yeast and more recent studies in Drosophila and mammalian systems. These studies suggest that unequal crossover is the major driving force in the evolution of the rRNA genes with sister chromatid exchange occurring more often than exchange between homologs. Gene conversion is also believed to play a role; however, direct evidence for its involvement has not been obtained. Remarkably, concerted evolution is so well orchestrated that even transposable elements that insert into a large fraction of the rRNA genes appear to have little effect on the process. Finally, we summarize data that suggest that recombination in the rDNA locus of higher eukaryotes is sufficiently frequent to monitor changes within a few generations.
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            Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

            Background The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse et al. in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments. Results We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables. Conclusions The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.
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              Rapid evolution to terrestrial life in Jamaican crabs

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                Author and article information

                Contributors
                andrey.rozenberg@rub.de , jaera@yandex.com
                pbrand@ucdavis.edu
                Nicole.Rivera@biologie.uni-regensburg.de
                Florian.Leese@rub.de
                Christoph.Schubart@biologie.uni-regensburg.de
                Journal
                BMC Evol Biol
                BMC Evol. Biol
                BMC Evolutionary Biology
                BioMed Central (London )
                1471-2148
                19 July 2015
                19 July 2015
                2015
                : 15
                : 142
                Affiliations
                [ ]Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany
                [ ]University of Regensburg, Department of Zoology and Evolutionary Biology, Regensburg, Germany
                [ ]University of California, Davis, Department of Evolution and Ecology, Center for Population Biology, Davis, USA
                Author information
                http://orcid.org/0000-0001-9534-2297
                Article
                380
                10.1186/s12862-015-0380-7
                4506587
                26187050
                ebc3a038-cb64-45a6-8418-ce8062abc819
                © Rozenberg et al. 2015

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 5 May 2015
                : 13 May 2015
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2015

                Evolutionary Biology
                nimaviridae,wssv,white spot syndrome virus,endogenized viruses,paleovirology
                Evolutionary Biology
                nimaviridae, wssv, white spot syndrome virus, endogenized viruses, paleovirology

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