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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
Article

Abstract

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.

Keywords

Populus NBS-LRR Resistance 

Notes

Acknowledgements

The Populus genome sequence data was produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/). 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)

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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

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