Molecular Evolution and Horizontal Gene Transfer in Plant Parasitic Nematodes

Abstract

Most evolutionary analyses of plant-parasitic nematodes have been based on a small number character sets and have provided little insight into the evolution of parasitism within the species analyzed. I have designed a strategy to recover the most robust phylogeny for five Meloidogyne species (M. arenaria, M. chitwoodi, M. hapla, M. incognita, and M. javanica), three closely related taxa (Heterodera glycines, Globodera pallida and G. rostochiensis) and the more distant taxon, C. elegans. The multiple-gene approach is based on sampling more than 80,000 tylenchid sequences present in public databases. I identified 47 genes which could unambiguously be assigned as orthologues, and performed an alignment, so that all 47 genes could be concatenated to create one multi-gene alignment. Bayesian analysis places M. incognita and M. javanica as sister taxa, with M. arenaria basal to these. Placement of M. hapla and M. chitwoodi are congruent with previous studies, as are relationships with the other taxa examined.

A method for a high-throughput genome screen for horizontally acquired genes is further presented, illustrated using expressed sequence tag (EST) data from M. incognita, M. javanica and M. arenaria. Applying a phylogenetic filter to a series of homology searches revealed previously postulated horizontally transferred genes and six new candidates. 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. Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism.