Research

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

Elizabeth H Scholl^1,2, Jeffrey L Thorne², James P McCarter^3,4 and David Mck Bird^1,2

¹Center for the Biology of Nematode Parasitism, Box 7253, North Carolina State University, Raleigh, NC 27695, USA

²Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, NC 27695, USA

³Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St. Louis, MO 63108, USA

⁴Divergence Inc., 893 North Warson Road, St. Louis, MO 63141, USA

author email corresponding author email

Genome Biology 2003, 4:R39doi:10.1186/gb-2003-4-6-r39

Published:	19 May 2003

Subject areas: Plant biology, Microbiology and parasitology, Evolution, Genome studies

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.