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

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.

Figure 1

Schematic species tree indicating relationships between bacteria, Drosophila, C. elegans and plant-parasitic nematodes in the family Heteroderidae. The locations of three possible horizontal gene-transfer events that would pass through our initial phylogenetic filter are indicated by dotted lines. Transfer 'a' occurs after divergence of the lineages leading to C. elegans and Heteroderidae, transfer 'b' after divergence of root-knot nematodes and cyst nematodes, and transfer 'c' to the lineage leading to a specific Meloidogyne species. Adapted from [59].

Figure 2

Cladogram of NodL-like proteins. The unrooted tree is generated by protein-distance and neighbor-joining methods and shows relationships of the deduced, putative Meloidogyne NodL proteins with similar enzymes, color-coded according to known function. Numbers indicate percent support from 1,000 non-parametric bootstrap replicates [53]. The scale bar represents 0.1 amino-acid replacements per site across the length of a given branch.

Figure 3

Structure of Meloidogyne incognita NodL and its deduced translation product. Features of the genomic sequence were established by comparison with that of a full-length cDNA clone, and are indicated by arrows in the following order: addition site of SL-1 trans-splice leader; beginning of intron; end of intron; and site of poly(A) tail.

Figure 4

Schematic map (not to scale) of four genes on the Mesorhizobium loti linear chromosome with putative homologs in M. incognita, encoding NodL, L-threonine aldolase, glutamine synthetase and an unknown function. Also indicated is the 612 kb transferable M. loti symbiosis island.