title: Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana.
abstract: BACKGROUND
  Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds.
  
  
  RESULTS
  We have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation.
  
  
  CONCLUSIONS
  The presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.
authors.affiliation: Dept of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA. mudge002@umn.edu
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.forename: Peter
authors.initials: P
authors.lastname: Kalo
authors.forename: Giles E D
authors.initials: GE
authors.lastname: Oldroyd
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Roe
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D046913:Medicago truncatula / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013025:Glycine max / Q000235:genetics*; D026801:Synteny; D020080:Tandem Repeat Sequences