Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana

Extended comparison of gene sequences found on homeologous soybean Bacterial Artificial Chromosomes to Medicago truncatula andArabidopsis thaliana genomic sequences demonstrated a network of synteny within conserved regions interrupted by gene addition and/or deletions. Consolidation of gene order among all 3 species provides a picture of ancestral gene order. The observation supports a genome history of fractionation resulting from gene loss/addition and rearrangement. In all 3 species, clusters ofN-hydroxycinnamoyl/benzoyltransferase genes were identified in tandemly duplicated clusters. Parsimony-based gene trees suggest that the genes within the arrays have independently undergone tandem duplication in each species. Genetic colinearity and orthology has traditionally been identified through comparative mapping. Whereas marker colinearity has been highly conserved in the grasses (Ahn and Tanksley 1993; Devos and Gale 2000), in the legumes synteny has often been fragmented. Early marker studies identified conserved syntenic blocks among various legume genera, Glycine max, Pisum sativum, and Vigna radiata (Menancio-Hautea et al. 1993; Boutin et al. 1995). Choi, Kim et al. and Choi, Mu