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      Detection and Characterization of Wolbachia Infections in Natural Populations of Aphids: Is the Hidden Diversity Fully Unraveled?

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          Abstract

          Aphids are a serious threat to agriculture, despite being a rather small group of insects. The about 4,000 species worldwide engage in highly interesting and complex relationships with their microbial fauna. One of the key symbionts in arthropods is Wolbachia, an α-Proteobacterium implicated in many important biological processes and believed to be a potential tool for biological control. Aphids were thought not to harbour Wolbachia; however, current data suggest that its presence in aphids has been missed, probably due to the low titre of the infection and/or to the high divergence of the Wolbachia strains of aphids. The goal of the present study is to map the Wolbachia infection status of natural aphids populations, along with the characterization of the detected Wolbachia strains. Out of 425 samples from Spain, Portugal, Greece, Israel and Iran, 37 were found to be infected. Our results, based mainly on 16S rRNA gene sequencing, indicate the presence of two new Wolbachia supergroups prevailing in aphids, along with some strains belonging either to supergroup B or to supergroup A.

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          Most cited references 133

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

           Robert Edgar (2004)
          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

            The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
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              MrBayes 3: Bayesian phylogenetic inference under mixed models.

              MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                13 December 2011
                : 6
                : 12
                Affiliations
                [1 ]Department of Environmental and Natural Resources Management, University of Ioannina, Agrinio, Greece
                [2 ]Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain
                [3 ]ISOPlexis Gene Bank, Universidade da Madeira, Funchal, Portugal
                [4 ]Department of Greenhouse Crops and Floriculture, Technological Educational Institute of Messolonghi, Messolonghi, Greece
                [5 ]Laboratório de Qualidade Agrícola, Núcleo de Fitopatologia,, Madeira, Portugal
                [6 ]Departamento de Ciências Agrárias CITA-A (Azorean Biodiversity Group), Universidade dos Açores, Angra do Heroísmo, Terceira – Azores
                [7 ]Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Valencia, Spain
                [8 ]Biomedical Sciences Research Center Al. Fleming, Vari, Greece
                [9 ]Department of Environmental and Natural Resources Management, University of Western Greece, Agrinio, Greece
                University of Poitiers, France
                Author notes

                Conceived and designed the experiments: KB AL MK GT. Performed the experiments: AAA DSG ED MM AP MS VD SR AFA GT. Analyzed the data: AAA DSG MM AL MK GT KB. Contributed reagents/materials/analysis tools: KB AL MK AP AFA PAVB GT. Wrote the paper: KB AAA AL MK GT.

                Article
                PONE-D-11-16968
                10.1371/journal.pone.0028695
                3236762
                22174869
                Augustinos et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                Page count
                Pages: 11
                Categories
                Research Article
                Agriculture
                Agroecology
                Agro-Population Ecology
                Biology
                Evolutionary Biology
                Organismal Evolution
                Microbial Evolution
                Microbiology
                Bacteriology
                Bacterial Taxonomy
                Microbial Ecology
                Microbial Evolution
                Zoology
                Entomology

                Uncategorized

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