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Molecular Characterization and Variation of the Broad bean wilt virus 2 Isolates Based on Analyses of Complete Genome Sequences

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      The full-genome sequences of fourteen isolates of Broad bean wilt virus 2 (BBWV2), collected from broad bean, pea, spinach, bell pepper and paprika plants in Korea during the years 2006–2012, were determined and analyzed comparatively along with fifteen previously reported BBWV2 genome sequences. Sequence analyses showed that RNA-1 and RNA-2 sequences of BBWV2 Korean isolates consisted of 5950–5956 and 3568–3604 nucleotides, respectively. Full-length genome sequence-based phylogenetic analyses revealed that the BBWV2 Korean isolates could be divided into three major groups comprising GS-I (isolates BB2 and RP7) along with isolate IP, GS-II (isolates BB5, P2, P3 and RP3) along with isolate B935, and GS-III including 16 BBWV2 Korean isolates. Interestingly, GS-III appears to be newly emerged and predominant in Korea. Recombination analyses identified two recombination events in the analyzed BBWV2 population: one in the RNA-1 of isolate K and another one in the RNA-2 of isolate XJ14-3. However, no recombination events were detected in the other 21 Korean isolates. On the other hand, out of 29 BBWV2 isolates, 16 isolates were found to be reassortants, of which each RNA segment ( i.e. RNA1 and RNA2) was originated from different parental isolates. Our findings suggested that reassortment rather than recombination is a major evolutionary force in the genetic diversification of BBWV population in Korea.

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      MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

      Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from
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        Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences.

        To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals. We have developed a method, that we call 'sister-scanning', for assessing phylogenetic and compositional signals in the various patterns of identity that occur between four nucleotide sequences. A Monte Carlo randomization is done for all columns (positions) within a window and Z-scores are obtained for four real sequences or three real sequences with an outlier that is also randomized. The usefulness of the approach is demonstrated using tobamovirus and luteovirus sequences. Contradictory phylogenetic signals were distinguished in both datasets, as were regions of sequence that contained no clear signal or potentially misleading signals related to compositional similarities. In the tobamovirus dataset, contradictory phylogenetic signals were separated by coding sequences up to a kilobase long that contained no clear signal. Our re-analysis of this dataset using sister-scanning also yielded the first evidence known to us of an inter-species recombination site within a viral RNA-dependent RNA polymerase gene together with evidence of an unusual pattern of conservation in the three codon positions.
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            Author and article information

            [1 ]Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
            [2 ]Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
            [3 ]Department of Plant Medicine, Chungbuk National University, Cheongju 361-763, Korea
            Author notes
            [* ]Corresponding author. Phone) +82-43-261-2557, FAX) +82-43-271-4414 E-mail) bjcha@
            Plant Pathol J
            Plant Pathol. J
            The Plant Pathology Journal
            Korean Society of Plant Pathology
            December 2013
            : 29
            : 4
            : 397-409
            4174820 10.5423/PPJ.OA.03.2013.0036 ppj-29-397
            ©The Korean Society of Plant Pathology

            This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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