title: Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization.
abstract: Arabidopsis and Medicago truncatula represent sister clades within the dicot subclass Rosidae. We used genetic map-based and bacterial artificial chromosome sequence-based approaches to estimate the level of synteny between the genomes of these model plant species. Mapping of 82 tentative orthologous gene pairs reveals a lack of extended macrosynteny between the two genomes, although marker collinearity is frequently observed over small genetic intervals. Divergence estimates based on non-synonymous nucleotide substitutions suggest that a majority of the genes under analysis have experienced duplication in Arabidopsis subsequent to divergence of the two genomes, potentially confounding synteny analysis. Moreover, in cases of localized synteny, genetically linked loci in M. truncatula often share multiple points of synteny with Arabidopsis; this latter observation is consistent with the large number of segmental duplications that compose the Arabidopsis genome. More detailed analysis, based on complete sequencing and annotation of three M. truncatula bacterial artificial chromosome contigs suggests that the two genomes are related by networks of microsynteny that are often highly degenerate. In some cases, the erosion of microsynteny could be ascribed to the selective gene loss from duplicated loci, whereas in other cases, it is due to the absence of close homologs of M. truncatula genes in Arabidopsis.
authors.affiliation: Department of Plant Pathology, University of California, Davis, California 95616, USA.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Zhu
authors.forename: Dong-Jin
authors.initials: DJ
authors.lastname: Kim
authors.forename: Jong-Min
authors.initials: JM
authors.lastname: Baek
authors.forename: Hong-Kyu
authors.initials: HK
authors.lastname: Choi
authors.forename: Leland C
authors.initials: LC
authors.lastname: Ellis
authors.forename: Helge
authors.initials: H
authors.lastname: Küester
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Hui-Mei
authors.initials: HM
authors.lastname: Peng
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D003001:Cloning, Molecular; D020440:Gene Duplication; D023061:Gene Order / Q000235:genetics; D008040:Genetic Linkage / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant; D029902:Medicago / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D013045:Species Specificity; D026801:Synteny