Plant Molecular Biology

, Volume 66, Issue 6, pp 619–636 | Cite as

Genome-wide identification of NBS resistance genes in Populus trichocarpa

  • Annegret Kohler
  • Cécile Rinaldi
  • Sébastien Duplessis
  • Marie Baucher
  • Danny Geelen
  • Frédéric Duchaussoy
  • Blake C. Meyers
  • Wout Boerjan
  • Francis Martin


As the largest class of disease resistance R genes, the genes encoding nucleotide binding site and leucine-rich repeat proteins (“NBS-LRR genes”) play a critical role in defending plants from a multitude of pathogens and pests. The diversity of NBS-LRR genes was examined in the Populus trichocarpa draft genome sequence. The NBS class of genes in this perennial tree is large and diverse, comprised of ∼400 genes, at least twice the complement of Arabidopsis. The NBS family can be divided into multiple subfamilies with distinct domain organizations. It includes 119 Coiled-Coil-NBS-LRR genes, 64 TIR-NBS-LRR genes, 34 BED-finger-NBS-LRR, and both truncated and unusual NBS- and NBS-LRR-containing genes. The transcripts of only 34 NBS-LRR genes were detected in rust-infected and non-infected leaves using a whole-genome oligoarray. None showed an altered expression two days post inoculation.


Populus NBS-LRR Resistance 



The Populus genome sequence data was produced by the US Department of Energy Joint Genome Institute ( We thank Daniel Rokshar and the other members of the Populus sequencing project at the JGI, and Jerry Tuskan (Oak Ridge National Laboratory) for permission to use the draft genome sequence before publication. Thanks to Uffe Hellsten and Stephen DiFazio for the duplication dataset. Annegret Kohler was supported by Postdoctoral Fellowships from the INRA, the Région Lorraine and the EU POPYOMICS FP6 programme. Cécile Rinaldi was supported by a joint doctoral scholarship from the INRA and the Région Lorraine and Sébastien Duplessis was supported by a junior scientist support grant from the Région Lorraine. Marie Baucher is a Research Associate from the Belgian National Funds for the Scientific Research (FNRS). This work received support from the INRA and the Belgian ‘Fonds de la Recherche Fondamentale Collective’ (No. 2.4524.02). The EST ub48dpf09 containing the NLS region was kindly provided by Dr. Stefan Jansson (Umea Plant Genetic Center, Umeå, Sweden).

Supplementary material

11103_2008_9293_MOESM1_ESM.ppt (38 kb)
Supplemental Fig. 1 Maximum parsimony trees of the different families of NBS proteins in Populus trichocarpa Nisqually-1. (a) Non-TIR-NBS-LRR proteins; (b) TIR-NBS-LRR and (c) Non-TIR-NBS and TIR-NBS. The trees were constructed using the NBS domain from the R proteins belonging to the different classes. The Arabidopsis and rice R protein with the highest similiarity from the Blast analysis as well as some other well-characterized R proteins from Arabidopsis and rice were included in the analysis. Sequence similarities to Arabidopsis subclasses are indicated in italic. Predicted proteins are designated according to their JGI Populus Genome Database entry codes, omitting the Poptr1_1: prefix. P25941 from Streptomyces rooted the trees as outgroup. (PPT 38 kb)
11103_2008_9293_MOESM2_ESM.ppt (34 kb)
(PPT 34 kb)
11103_2008_9293_MOESM3_ESM.ppt (30 kb)
(PPT 30 kb)
11103_2008_9293_MOESM4_ESM.rtf (19 kb)
Supplemental Fig. 2 Multiple sequence alignment of the Populus BNL proteins containing the zinc-finger BED/DUF1544 domains (IPRO003656/IPR011523) with the BED finger domains found in proteins from other plants and animals. The conserved signature Cx2CxnHx3-5[H/C] and the highly conserved N-terminal aromatic positions of the BED finger are shown in red and blue letters, respectively, and are indicated by triangles and stars. Examples from Arabidopsis, rice, maize as well as from animals and human from INTERPRO were compared to Populus BNLs (Poptr1_1:573542 and Poptr1_1:596247, amino acid sequences in bold letters) and other Populus predicted BED finger domain containing proteins (Poptr1_1:750729 TAM3 transposase, Poptr1_1:795076 hAT dimerisation domain containing protein and Poptr1_1:796265 Zn finger protein). (RTF 19 kb)
11103_2008_9293_MOESM5_ESM.rtf (4 kb)
Supplemental Fig. 3 Alignment of parts of the deduced amino acid sequences from the Populus tremula EST UB48DPF09 and five predicted TNL proteins from P. trichocarpa. The conserved nuclear localisation sequence is indicated by a bar (RTF 5 kb)
11103_2008_9293_MOESM6_ESM.xls (236 kb)
Supplemental table 1 List of gene models encoding NBS protein in P. trichocarpa. A complete list of all predicted Populus NBS genes as well as their classification, EST support, expression on the NimbleGen arrays, location, additional domains and intron numbers. (XLS 237 kb)
11103_2008_9293_MOESM7_ESM.xls (124 kb)
Supplemental table 2 BlastP of the putative Populus NBS proteins against the Arabidopsis and rice proteomes. A BlastP search was used to compare the NBS part as well as the complete sequence of the predicted Populus R proteins to the Arabidopsis and rice proteomes. The best BlastP result with the e-value is given in the list. (XLS 125 kb)
11103_2008_9293_MOESM8_ESM.xls (124 kb)
Supplemental table 3 Summary table of MEME and MAST analyses for CN/CNL (a), TN/TNL/TNLT/TNLN (b), BN/BNL (c) and N/NL (d) proteins. Motifs from the MEME analyses were combined and manually aligned in a spreadsheet to allow the comparisons of motif composition and configuration. Because motif analyses were performed for each domain separately for each of the protein families, motif numbers are specific only to that domain. The MEME “score” for the overall match of the protein to the motif models is given as a P-value. (XLS 124 kb)
11103_2008_9293_MOESM9_ESM.xls (82 kb)
(XLS 82 kb)
11103_2008_9293_MOESM10_ESM.xls (44 kb)
(XLS 44 kb)
11103_2008_9293_MOESM11_ESM.xls (72 kb)
(XLS 73 kb)
11103_2008_9293_MOESM12_ESM.rtf (10 kb)
Supplemental table 4 Number of clusters and the total number of corresponding NBS genes for each type of clusters in Populus trichocarpa ‘Nisqually-1’ genome sequence. Consecutive NBS-genes separated by 8 -or less- other genes were considered as clusters, as reported in Richly et al. (2002) and Meyers et al. (2003). The number of clusters and NBS-genes which were found on linkage groups are in brackets. Singletons are also indicated (RTF 11 kb)


  1. Ameline-Torregrosa C, Wang BB, O’Bleness MS et al (2007) Identification and Characterization of NBS-LRR Genes in the Model Plant Medicago truncatula. Plant Physiol Prev. doi:  10.1104/pp.107.104588
  2. Aravind L (2000) The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases. Trends Biochem Sci 25:421–423PubMedCrossRefGoogle Scholar
  3. Ayliffe MA, Lagudah ES (2004) Molecular genetics of disease resistance in cereals. Ann Bot 94:765–773PubMedCrossRefGoogle Scholar
  4. Bai J, Pennill LA, Ning J et al (2002) Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res 12:1871–1884PubMedCrossRefGoogle Scholar
  5. Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3:21–29PubMedGoogle Scholar
  6. Bailey TL, Gribskov M (1998) Methods and statistics for combining motif match scores. J Comput Biol 5:211–221PubMedCrossRefGoogle Scholar
  7. Baumgarten A, Cannon S, Spangler R et al (2003) Genome-level evolution of resistance genes in Arabidopsis thaliana. Genetics 165:309–319PubMedGoogle Scholar
  8. Belkhadir Y, Subramaniam R, Dangl JL (2004) Plant disease resistance protein signaling: NBS-LRR proteins and their partners. Curr Opin Plant Biol 7(4):391–399PubMedCrossRefGoogle Scholar
  9. Burch-Smith TM, Schiff M, Caplan JL et al (2007) A novel role for the TIR domain in association with pathogen-cerived elicitors. PloS Biol 13:e68CrossRefGoogle Scholar
  10. Cervera MT, Storme V, Ivens B et al (2001) Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158:787–809PubMedGoogle Scholar
  11. Chini A, Grant JJ, Seki M et al (2004) Drought tolerance established by enhanced expression of the CC-NBS-LRR gene, ADR1, requires salicylic acid, EDS1 and ABI1. Plant J 38:810–822PubMedCrossRefGoogle Scholar
  12. Chini A, Loake GJ (2005) Motifs specific for the ADR1 NBS-LRR protein family in Arabidopsis are conserved among NBS-LRR sequences from both dicotyledonous and monocotyledonous plants. Planta 221:597–601PubMedCrossRefGoogle Scholar
  13. Dangl JL, Jones JDG (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833PubMedCrossRefGoogle Scholar
  14. Deslandes L, Olivier J, Peeters N et al (2003) Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proc Natl Acad Sci USA 100:8024–8029PubMedCrossRefGoogle Scholar
  15. Faigon-Soverna A, Harmon FG, Storani L et al (2006) A constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development. Plant Cell 18:2919–2928PubMedCrossRefGoogle Scholar
  16. Geelen DNV, Inzé DG (2001) A bright future for the Bright Yellow-2 cell culture. Plant Physiol 127:1375-1379PubMedCrossRefGoogle Scholar
  17. Jeanmougin F, Thompson JD, Gouy M et al (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403–405PubMedCrossRefGoogle Scholar
  18. Jorge V, Dowkiw A, Faivre-Rampant P et al (2005) Genetic architecture of qualitative and quantitative Melampsora larici-populina leaf rust resistance in hybrid poplar: genetic mapping and QTL detection. New Phytol 167:113–127PubMedCrossRefGoogle Scholar
  19. Karimi M, Inzé D, Depicker A (2002) GATEWAY™ vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193–195PubMedCrossRefGoogle Scholar
  20. Kelleher CT, Chiu R, Shin H et al (2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J 50:1063–1078PubMedCrossRefGoogle Scholar
  21. Lahaye T (2002) The Arabidopsis RRS1-R disease resistance gene-uncovering the plant’s nucleus as the new battlefield of plant defense? Trends Plant Sci 7:425–427PubMedCrossRefGoogle Scholar
  22. Lescot M, Rombauts S, Zhang J et al (2004) Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and II transposable elements. Theor Appl Genet 109:10–22PubMedCrossRefGoogle Scholar
  23. Liu JJ, Ekramoddoullah AKM (2003) Isolation, genetic variation and expression of TIR-NBS-LRR resistance gene analogs from western white pine (Pinus monticola Dougl.ex.D.Don). Mol Gen Genomics 270:432–441CrossRefGoogle Scholar
  24. Liu JJ, Ekramoddoullah AKM (2007) The CC-NBS-LRR subfamily in Pinus monticola: targeted identification, gene EXPRESSION, and genetic linkage with resistance to Cronartium ribicola. Phytopathology 97:728–736CrossRefPubMedGoogle Scholar
  25. Lupas A, Van Dyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164CrossRefGoogle Scholar
  26. McDowell JM, Woffenden BJ (2003) Plant disease resistance genes: recent insights and potential applications. Trends Biotech 21:178–183CrossRefGoogle Scholar
  27. Meyers BC, Dikerman AW, Michelmore RW et al (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:31732CrossRefGoogle Scholar
  28. Meyers BC, Morgante M, Michelmore RW (2002) TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. Plant J 32:77–92PubMedCrossRefGoogle Scholar
  29. Meyers BC, Kozik A, Griego A et al (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15:809–834PubMedCrossRefGoogle Scholar
  30. Meyers BC, Kaushik S, Nandety RS (2005) Evolving disease resistance genes. Curr Opin Plant Biol 8:129–134PubMedCrossRefGoogle Scholar
  31. Mondragón-Palomino M, Meyers BC, Michelmore RW et al (2002) Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res 12:1305–1315PubMedCrossRefGoogle Scholar
  32. Nagata T, Nemoto Y, Hasezawa S (1992) Tobacco BY-2 cell line as the “HeLa” cell in the cell biology of higher plants. Int Rev Cytol 132:1-30Google Scholar
  33. Noel L, Moores TL, van der Biezen EA et al (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11:2099–2111PubMedCrossRefGoogle Scholar
  34. Ralph S, Oddy C, Cooper D et al (2006) Genomics of hybrid poplar (Populus trichocarpa × deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences. Mol Ecol 15:1275–1297PubMedCrossRefGoogle Scholar
  35. Richly E, Kurth J, Leister D (2002) Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol Biol Evol 19:76–84PubMedGoogle Scholar
  36. Rinaldi C, Kohler A, Frey P et al (2007) Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol 144:347–366PubMedCrossRefGoogle Scholar
  37. Schwartz S, Zhang Z, Frazer KA et al (2000) PipMakerA web server for aligning two genomic DNA sequences. Genome Res 10:577–586PubMedCrossRefGoogle Scholar
  38. Shen QH, Saijo Y, Mauch S et al (2007) Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. Science 315:1098–1103PubMedCrossRefGoogle Scholar
  39. Swofford DL (1999) PAUP*. Phylogenetic analysis using parsimony (*and other methods) Version 4. Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
  40. Tan S, Meyers BC, Kozik A et al (2007) Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biol 7:56PubMedCrossRefGoogle Scholar
  41. Tuskan G, DiFazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa. Science 313:1596–1604PubMedCrossRefGoogle Scholar
  42. Wirthmueller L, Zhang Y, Jones JDG et al (2007) Nuclear accumulation of the Arabidopsis immune receptor RPS4 is necessary fr triggering EDS1-dependant defense. Curr Biol 17:2023–2029PubMedCrossRefGoogle Scholar
  43. Yin TM, DiFazio SP, Gunter LE et al (2004) Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence. New Phytol 164: 95–105CrossRefGoogle Scholar
  44. Zhang Y, Li X (2005) A putative nucleoporin 96 is required for both basal defense and constitutive resistance responses mediated by suppressor of npr1-1, constitutive 1. Plant Cell 17:1306–1316PubMedCrossRefGoogle Scholar
  45. Zhang J, Steenackers M, Storme V et al (2001) Fine mapping and identification of nucleotide binding site/leucine-rich repeat sequences at the MER locus in Populus deltoides ‘S9-2’. Phytopathology 91:1069–1073CrossRefPubMedGoogle Scholar
  46. Zhou T, Wang JQ, Chen JQ et al (2004) Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics 271:402–415PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Annegret Kohler
    • 1
  • Cécile Rinaldi
    • 1
  • Sébastien Duplessis
    • 1
  • Marie Baucher
    • 2
  • Danny Geelen
    • 3
  • Frédéric Duchaussoy
    • 1
  • Blake C. Meyers
    • 4
  • Wout Boerjan
    • 5
    • 6
  • Francis Martin
    • 1
  1. 1.Unité Mixte de Recherche INRA/UHP 1136 Interactions Arbres/MicroorganismesInstitut National de la Recherche Agronomique, Centre de Recherches de NancyChampenouxFrance
  2. 2.Laboratoire de Biotechnologie VégétaleUniversité Libre de BruxellesGosseliesBelgium
  3. 3.Department of Plant Production, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
  4. 4.Department of Plant and Soil SciencesDelaware Biotechnology Institute, Delaware Technology ParkNewarkUSA
  5. 5.Department of Plant Systems BiologyFlanders Institute for BiotechnologyGentBelgium
  6. 6.Department of Molecular GeneticsGhent UniversityGentBelgium

Personalised recommendations