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GENOME ANALYSIS

Identification and Characterization of Nucleotide-Binding Site-Leucine-Rich Repeat Genes in the Model Plant Medicago truncatula^1,[W],[OA]

Laboratoire des Interactions Plantes Microorganismes, UMR CNRS-INRA 442–2594, 31326 Castanet Tolosan, France (C.A.-T.); Departments of Plant Pathology and Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., B.-B.W., N.D.Y.); Advanced Center for Genome Technology and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73109 (M.S.O., B.A.R.); Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546–0236 (H.Z.); and United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.B.C.)

The nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. We have identified 333 nonredundant NBS-LRRs in the current Medicago truncatula draft genome (Mt1.0), likely representing 400 to 500 NBS-LRRs in the full genome, or roughly 3 times the number present in Arabidopsis (Arabidopsis thaliana). Although many characteristics of the gene family are similar to those described on other plant genomes, several evolutionary features are particularly pronounced in M. truncatula, including a high degree of clustering, evidence of significant numbers of ectopic translocations from clusters to other parts of the genome, a small number of more evolutionarily stable NBS-LRRs, and numerous truncations and fusions leading to novel domain compositions. The gene family clearly has had a large impact on the structure of the genome, both through ectopic translocations (potentially, a means of seeding new NBS-LRR clusters), and through two extraordinarily large superclusters. Chromosome 6 encodes approximately 34% of all TIR-NBS-LRRs, while chromosome 3 encodes approximately 40% of all coiled-coil-NBS-LRRs. Almost all atypical domain combinations are in the TIR-NBS-LRR subfamily, with many occurring within one genomic cluster. This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Steven B. Cannon (steven.cannon@ars.usda.gov).

^[W] The online version of this article contains Web-only data.

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www.plantphysiol.org/cgi/doi/10.1104/pp.107.104588

^* Corresponding author; e-mail steven.cannon{at}ars.usda.gov.

Received June 25, 2007; accepted October 19, 2007; published November 2, 2007.

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