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  1. Genomic Organization Of Regions Containing Clusters Of NBS-LRR Genes In Medicago truncatulaShweta Deshpande , Majesta Seigfried , Fares Z. Najar, Hongshing Lai, Steve Kenton, and Bruce A. RoeDepartment of Chemistry and Biochemistry, Stephenson Research and Technology Center, University of Oklahoma, 101 David L. Boren Blvd, Norman, Oklahoma, 73019

  2. Abstract Our laboratory is a member of the international consortium sequencing the model legume, Medicago truncatula,. With over 1000 BACs sequenced representing approximately half of the euchromatic region, we now have begun our initial analysis focusing on the disease resistance genes with sequence homology to known NBS-LRR genes. Of the 604 BACs mapped to date, 70 of them contain clusters of NBS-LRR genes. Among these, 5 BACs that contained genomic regions with clustered NBS-LRR genes were examined in detail and revealed that each separate cluster has its own resistance specificity. These five clusters consist of two clusters on chromosome 4 each containing three genes which show sequence similarity to Nematode resistance-like protein from Solanum tuberasum, a cluster of four genes on chromosome 6 which show sequence similarity to Blight resistance protein B149 from Solanum bulbocastanum, and two clusters, one containing five genes and the other containing four genes, on chromosome 6 which show sequence similarity to KR1 resistance protein in Glycine max. Further analysis of the five gene, KR1 resistance protein cluster on chromosome 6 revealed that the five genes have high levels of conservation in their motifs but diverge in the flanking regions. Additional comparative analysis will be discussed.

  3. Why sequence the Medicago truncatulagenome? • A model legume, an economically important plant and a source of protein. • Has an ability to fix Nitrogen and hence improve soil fertility. • Synthesizes compounds which possess anti-cancer and other health promoting effects. • Has a small diploid genome (470 Mbp) with 8 chromosome. • Has a short seed to seed germination time.

  4. Understanding of plant disease resistance processes is important to improving crop yields. The superfamily of plant resistance genes, NBS-LRR is the largest and most common of disease resistance genes. NBS-LRR genes often are found clustered within regions of the genome, as a result of the evolutionary duplication processes that these genes undergo. NBS region are the ATP and GTP binding sites and they play a role in signal transduction. LRRs are responsible for the recognition and binding of ligands produced by pathogens. Plant Disease Resistance

  5. NBS-LRR • NBS-LRRs are grouped into two classes: • The presence of the N-terminal toll / Interleukin receptor (TIR) domain where toll is homologous to drosophila toll region and Interleukin receptor is similar to the mammalian interleukin receptor. • The other class is the non-TIR NBS-LRR it encodes a Coiled-Coil (CC) domain or Leucine Zipper (LZ) in their N-Terminal. • Structure of NBS-LRR : TIR domain ~ 200 amino acids. NBS domain ~ 300 amino acids. LRR domain ~ 10 – 40 leucines. (Kinase 1a) a a

  6. Clusters of NBS-LRR in the genome To date there are 49 contigs that contain clusters of NBS-LRR genes, spread over the genome. Among these contigs there are 70 BACs that contain clusters, totaling 335 clustered NBS-LRR genes. NBS-LRR

  7. ClustalW mth2-33o18 TIR Domain NBS Domain Kinase 1a Kinase 2a GLPL motif Trans-membrane Trans-membrane LRR Domain

  8. mth2-33o18 • Mth2-33o18, which maps to chromosome six in contig 276, contains a five gene cluster with homology to the Soybean KR1 gene. The Kefeng Resistance 1 (KR1) gene confers resistance to the Soybean mosaic virus, an economically damaging disease that causes legumes to produce fewer, smaller, and poor quality seeds • As shown in the previous slide, the genes in this cluster have highly conserved TIR and NBS domains, especially at the kinase motifs within the NBS domain. • The genes diverge in the LRR domain, the putative trans-membrane domains, and their non-domain regions, leading to divergence in their phylogenies. Chromosome 6

  9. ClustalW mth2-10d14 TIR Domain NBS Domain Kinase 1a Kinase 2a Trans-membrane GLPL-motif Trans-membrane LRR Domain

  10. mth2-10d14 • BAC mth2-10d14 maps to chromosome 6 in contig 1050 has a cluster of 4 putative KR1-like resistance genes. • As shown in the previous slide, like mth2-30o18, the genes have highly conserved TIR and NBS domains, especially at the Kinase motifs. • The genes diverge in the LRR domain, the putative trans-membrane domains, and their non-domain regions, leading to divergence in their phylogenies. Chromosome 6

  11. ClustalW mth2-20p12 LRR Domain NBS Domain Kinase 1a Kinase 2a Kinase 3a GLPL-motif

  12. mth2-20p12 • Blight resistance genes are resistant to oomycete pathogens, which attack the tubers and foliage during any stage of crop development. BAC mth2-20p12 is mapped to chromosome 6 on contig 54, has a cluster of 4 putative Blight resistant genes. • As shown in the previous slide, the genes in this cluster have a highly conserved NBS domain, especially at the kinase motifs. • The genes diverge at their LRR domain and non-domain sites, leading to divergence in their phylogenies. Chromosome 6

  13. ClustalW mth2-23l11 TIR Domain LRR domain Kinase 1a NBS Domain Kinase 2a Kinase 3a GLPL motif

  14. mth2-23l11 • Nematode resistance genes are genes which are resistant to Nematodes that affect the growth and development of plants by physically injuring the roots while feeding, penetrating and moving through them. BAC mth2-23l11, which maps to chromosome 4 on contig 65, has a cluster of 3 putative Nematode resistance genes. • As shown on the previous slide, the genes have highly conserved TIR and NBS domains, especially at the kinase motif. • The genes diverge in the LRR domain and their non-domain regions, leading to divergence in their phylogenies. Chromosome 6

  15. ClustalW mth2-28e19 TIR Domain LRR domain NBS Domain Kinase 1a Kinase 3a Kinase 2a GLPL motif

  16. mth2-28e19 • BAC mth2-28e19, which maps to chromosome 4 on contig 65, has a cluster of 4 putative Nematode resistance genes. • As shown in the previous slide, like mth2-23l11, the genes have a highly conserved NBS domain, especially at the Kinase motifs. • The genes diverge in the LRR domain, the TIR domain, and their non-domain regions, leading to divergence in their phylogenies. Chromosome 6

  17. Comparison of BAC mth2-10d14 with mth2-23L11 and mth2-33o18 mth2-10d14 mth2-23L11 mth2-33o18 Duplications of parts of existing NBS-LRR genes recombine to make different NBS-LRR genes.

  18. Conclusions • The gene clusters all show homology to the same disease resistance gene due to local duplications within the genome. • Comparison of the three BACs along with their phylogenetic studies revealed that exons of genes are duplicated and are rearranged resulting in gene divergence.

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