Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approachReport as inadecuate




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Genome Biology

, 4:R39

First Online: 19 May 2003Received: 31 January 2003Revised: 27 March 2003Accepted: 22 April 2003

Abstract

BackgroundPublished 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.

ResultsOur 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.

ConclusionsHigh-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.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2003-4-6-r39 contains supplementary material, which is available to authorized users.

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Author: Elizabeth H Scholl - Jeffrey L Thorne - James P McCarter - David Mck Bird

Source: https://link.springer.com/



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