Nuclear protein-coding genes in phylogeny reconstruction and homology assessment: some examples from Leguminosae

Nuclear, protein-coding genes present both advantages and disadvantages for plant systematists. Analyses of gene expression in a phylogenetic context may provide criteria for assessing homologies of structural or functional phenotypic characters. Recombination introduces technical and theoretical problems, but permits different nuclear genes to serve as independent historical markers, a feature that may be particularly critical in studies of closely related species. Because gene duplication has been and continues to be a major force in plant genome evolution, identifying orthologous sequences is an important concern. Concerted evolution can alleviate this problem, but varies in its effectiveness as a homogenizing agent not only across different gene families but also at different taxonomic levels and even from taxon to taxon in the same gene family. Among genes we are engaged in studying, the nuclear copy of the normally mitochondrially-encoded cytochrome oxidase subunit II (cox2) is a true single copy gene in some legumes, and has proven useful in studies of phylogeny within the papilionoid tribe Phaseoleae and allies. In studies of Glycine, introns of one member of the complex histone H3 gene family are more variable than nrDNA ITS sequences and at the same time more congruent with genomic relationships than is cpDNA. Genes encoding leghemoglobin vary in their degree of concerted evolution both across the Papilionoideae and within Phaseoleae, and represent a cautionary note about assumptions concerning this phenomenon. Glutamine synthetase genes have been used both for studies at lower taxonomic levels and also to address questions concerning the homologies of nodules in different legume subfamilies. The gene family seems to be much more complex than it appeared from studies of expressed sequences in pea or Phaseolus.