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Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach

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      Abstract

      A method for a high-throughput genome screening for horizontally acquired genes is presented, and is illustrated using EST data from three species of root-knot nematode, Meloidogyne species.

      Abstract

      Background

      Published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes. We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne species.

      Results

      Our approach identified the previously postulated horizontally transferred genes and revealed six new candidates. Screening was partially dependent on sequence quality, with more candidates identified from clustered sequences than from raw EST data. Computational and experimental methods verified the horizontal gene transfer candidates as bona fide nematode genes. Phylogenetic analysis implicated rhizobial ancestors as donors of horizontally acquired genes in Meloidogyne.

      Conclusions

      High-throughput genomic screening is an effective way to identify horizontal gene transfer candidates. Transferred genes that have undergone amelioration of nucleotide composition and codon bias have been identified using this approach. Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism.

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      Most cited references 60

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          The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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            Author and article information

            Affiliations
            [1 ]Center for the Biology of Nematode Parasitism, Box 7253, North Carolina State University, Raleigh, NC 27695, USA
            [2 ]Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, NC 27695, USA
            [3 ]Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St. Louis, MO 63108, USA
            [4 ]Divergence Inc., 893 North Warson Road, St. Louis, MO 63141, USA
            Contributors
            Journal
            Genome Biol
            Genome Biology
            BioMed Central (London )
            1465-6906
            1465-6914
            2003
            19 May 2003
            : 4
            : 6
            : R39
            193618
            gb-2003-4-6-r39
            12801413
            10.1186/gb-2003-4-6-r39
            Copyright © 2003 Scholl et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
            Categories
            Research

            Genetics

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