Abstract
While multiple genes are optimal for corroborating nematode phylogenies, only a few are commonly used. Here we examine the phylogenetic potential of the nuclear Hsp90 chaperone gene. We used degenerate primers to obtain partial Hsp90 sequences from several plant-parasitic and free-living nematodes. Hsp90 was single-copy in Heterodera glycines and Meloidogyne javanica, similar to the situation for Caenorhabditis elegans. The full-length H. glycines Hsp90 protein sequence showed homology to sequences from C. elegans and Brugia pahangi and to other eukaryotes, and contains several functionally important regions common to cytoplasmic Hsp90 proteins. The Hsp90 amino acid phylogeny supported the Coelomata hypothesis for metazoan evolution. Phylogenetic trees, substitution scatter plots, and statistics for phylogenetic signal were made for Hsp90, 18S small subunit (SSU), and 28S large subunit (LSU) over a limited but broad sampling of nematode taxa. Only the LSU data set failed to recover any of the expected topology and showed extensive substitution saturation. In an intensive sampling of plant-parasitic nematode taxa, the Hsp90 tree topologies were generally congruent with rDNA results and alignments were unambiguous. Hsp90 sequences may help strengthen branch support or clarify tree topologies when other molecules show ambiguous alignments, greater branch-length heterogeneity, or codon bias in certain taxonomic groups.