NEMATIC: A simple and versatile tool for the insilico analysis of plant-nematode interactions

Molecular Plant Pathology

Volumn 15, Issue 6, 2014, Pages 627-636

  Cabrera, Javier ^a   Bustos, Regla ^b   Favery, Bruno ^c   Fenoll, Carmen ^a   Escobar, Carolina ^a  

^a UNIVERSITY OF CASTILLA LA MANCHA   (Spain)

^b ETSI MontesTechnical University of Madrid   (Spain)

^c Institut Sophia Agrobiotech   (France)

Author keywords

Functional classification; Galls; Giant cells; insilico analysis; Plant nematode interactions; Syncytia; Transcriptome comparison

Indexed keywords

ARABIDOPSIS; MELOIDOGYNE; NEMATODA;

INDOLEACETIC ACID DERIVATIVE; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ANIMAL; ARABIDOPSIS; BIOSYNTHESIS; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SCREENING; HOST PATHOGEN INTERACTION; METABOLISM; NEMATODE; PARASITOLOGY; PATHOGENICITY; PLANT DISEASE; PLANT GENE; STATISTICS AND NUMERICAL DATA; TYLENCHOIDEA;

ANIMALS; ARABIDOPSIS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENES, PLANT; HIGH-THROUGHPUT SCREENING ASSAYS; HOST-PATHOGEN INTERACTIONS; INDOLEACETIC ACIDS; NEMATODA; PLANT DISEASES; PLANT PROTEINS; SOFTWARE; TRANSCRIPTION FACTORS; TYLENCHOIDEA;

EID: 84903984157     PISSN: 14646722     EISSN: 13643703     Source Type: Journal    
DOI: 10.1111/mpp.12114     Document Type: Article

References (49)

1. Ali, M.A., Abbas, A., Kreil, D.P. and Bohlmann, H. (2013) Overexpression of the transcription factor RAP2.6 leads to enhanced callose deposition in syncytia and enhanced resistance against the beet cyst nematode Heterodera schachtii in Arabidopsis roots. BMC Plant Biol. 13, 47.
2. Alkharouf, N.W., Klink, V.P., Chouikha, I.B., Beard, H.S., MacDonald, M.H., Meyer, S., Knap, H.T., Khan, R. and Matthews, B.F. (2006) Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). Planta, 224, 838-852.
3. de Almeida Engler, J. and Favery, B. (2011) The plant cytoskeleton remodelling in nematode induced feeding sites. In: Genomics and Molecular Genetics of Plant-Nematode Interactions (Jones, J., Gheysen, G. and Fenoll, C., eds), pp. 369-394. Dordrecht: Springer.
4. de Almeida Engler, J., Kyndt, T., Vieira, P., Van Cappelle, E., Boudolf, V., Sanchez, V., Escobar, C., De Veylder, L., Engler, G., Abad, P. and Gheysen, G. (2012) CCS52 and DEL1 genes are key components of the endocycle in nematode-induced feeding sites. Plant J. 72, 185-198.
5. Barcala, M., Garcia, A., Cabrera, J., Casson, S., Lindsey, K., Favery, B., García-Casado, G., Solano, R., Fenoll, C. and Escobar, C. (2010) Early transcriptomic events in microdissected Arabidopsis nematode-induced giant cells. Plant J. 61, 698-712.
6. Barthels, N., van der Lee, F.M., Klap, J., Goddijn, O.J., Karimi, M., Puzio, P., Grundler, F.M., Ohl, S.A., Lindsey, K., Robertson, L., Robertson, W.M., Van Montagu, M., Gheysen, G. and Sijmons, P.C. (1997) Regulatory sequences of Arabidopsis drive reporter gene expression in nematode feeding structures. Plant Cell, 9, 2119-2134.
7. Berckmans, B., Vassileva, V., Schmid, S.P.C., Maes, S., Parizot, B., Naramoto, S., Magyar, Z., Alvim Kamei, C.L., Koncz, C., Bögre, L., Persiau, G., De Jaeger, G., Friml, J., Simon, R., Beeckman, T. and De Veylder, L. (2011) Auxin-dependent cell cycle reactivation through transcriptional regulation of Arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell, 23, 3671-3683.
8. Bird, D.M. (1996) Manipulation of host gene expression by root-knot nematodes. J. Parasitol. 82, 881-888.
9. Brady, S.M., Orlando, D.A., Lee, J.Y., Wang, J.Y., Koch, J., Dinneny, J.R., Mace, D, Ohler, U. and Benfey, P.N. (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science, 318, 801-806.
10. Caillaud, M.C., Dubreuil, G., Quentin, M., Perfus-Barbeoch, L., Lecomte, P., de Almeida Engler, J., Abad, P., Rosso, M.N. and Favery, B. (2008) Root-knot nematodes manipulate plant cell functions during a compatible interaction. J. Plant Physiol. 165, 104-113.
11. Damiani, I., Baldacci-Cresp, F., Hopkins, J., Andrio, E., Balzergue, S., Lecomte, P., Puppo, A., Abad, P., Favery, B. and Hérouart, D. (2012) Plant genes involved in harbouring symbiotic rhizobia or pathogenic nematodes. New Phytol. 194, 511-522.
12. Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M. and Grotewold, E. (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics, 4, 25.
13. Escobar, C., Brown, S. and Mitchum, M.G. (2011) Transcriptomic and proteomic analysis of the plant response to nematode infection. In: Genomics and Molecular Genetics of Plant-Nematode Interactions (Jones, J., Gheysen, G. and Fenoll, C., eds), pp. 157-174. Dordrecht: Springer.
14. Fuller, V.L., Lilley, C.J., Atkinson, H.J. and Urwin, P.E. (2007) Differential gene expression in Arabidopsis following infection by plant-parasitic nematodes Meloidogyne incognita and Heterodera schachtii. Mol. Plant Pathol. 8, 2-4.
15. Gheysen, G. and Fenoll, C. (2002) Gene expresion in nematode feeding sites. Annu. Rev. Phytopathol. 40, 191-219.
16. Gheysen, G. and Mitchum, M.G. (2009) Molecular insights in the susceptible plant response to nematode infection. In: Cell Biology of Plant Nematode Parasitism (Berg, R.H. and Taylor, C.G., eds), pp. 45-82. Heidelberg: Springer.
17. Goddijn, O.J., Lindsey, K., van der Lee, F.M., Klap, J.C. and Sijmons, P.C. (1993) Differential gene expression in nematode-induced feeding structures of transgenic plants harbouring promoter-gusA fusion constructs. Plant J. 4, 863-873.
18. Goverse, A. and Bird, D. (2011) The role of plant hormones in nematode feeding cell formation. In: Genomics and Molecular Genetics of Plant-Nematode Interactions (Jones, J., Gheysen, G. and Fenoll, C., eds), pp. 325-348. Dordrecht: Springer.
19. Grunewald, W., Karimi, M., Wieczorek, K., Van de Cappelle, E., Wischnitzki, E., Grundler, F., Inzé, D., Beeckman, T. and Gheysen, G. (2008) A role for AtWRKY23 in feeding site establishment of plant-parasitic nematodes. Plant Physiol. 148, 358-368.
20. Grunewald, W., van Noorden, G., Van Isterdael, G., Beeckman, T., Gheysen, G. and Mathesius, U. (2009) Manipulation of auxin transport in plant roots during Rhizobium symbiosis and nematode parasitism. Plant Cell, 21, 2553-2562.
21. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L. and Luo, J. (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics, 21, 2568-2569.
22. Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Oertle, L., Oertle, L., Widmayer, P., Gruissem, W. and Zimmermann, P. (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv. Bioinformatics, 2008, 420747.
23. Hussey, R.S. and Grundler, F.M. (1998) Nematode parasitism of plants. In: Physiology and Biochemistry of Free-living and Plant Parasitic Nematodes (Perry, R.N. and Wright, J., eds), pp. 213-243. Oxford: CAB International Press.
24. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. and Shinozaki, K. (2005) RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Res. 12, 247-256.
25. Ithal, N., Recknor, J., Nettleton, D., Maier, T., Baum, T.J. and Mitchum, M.G. (2007) Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Mol. Plant-Microbe Interact. 20, 510-525.
26. Jammes, F., Lecomte, P., de Almeida-Engler, J., Bitton, F., Martin-Magniette, M.L., Renou, J.P., Abad, P. and Favery, B. (2005) Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. Plant J. 44, 447-458.
27. Jones, M.G.K. (1981) Host cell responses to endoparasitic nematode attack: structure and function of giant cells and syncytia. Ann. Appl. Biol. 97, 353-372.
28. Jones, M.G.K. and Goto, D.B. (2011) Root-knot nematodes and giant cells. In: Genomics and Molecular Genetics of Plant-Nematode Interactions (Jones, J., Gheysen, G. and Fenoll, C., eds), pp. 83-102. Dordrecht: Springer.
29. Khan, R., Alkharouf, N., Beard, H., MacDonald, M., Chouikha, I., Meyer, S., Grefenstette, J., Knap, H. and Matthews, B. (2004) Microarray analysis of gene expression in soybean roots susceptible to the soybean cyst nematode two days post invasion. J. Nematol. 36, 241-248.
30. Klink, V.P., Overall, C.C., Alkharouf, N.W., MacDonald, M.H. and Matthews, B.F. (2007) Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Planta, 226, 1389-1409.
31. Klink, V.P., Hosseini, P., Matsye, P., Alkharouf, N.W. and Matthews, B.F. (2009) A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). Plant Mol. Biol. 71, 525-567.
32. Kyndt, T., Denil, S., Haegeman, A., Trooskens, G., Bauters, L., Van Criekinge, W., De Meyer, T. and Gheysen, G. (2012) Transcriptional reprogramming by root knot and migratory nematode infection in rice. New Phytol. 196, 887-900.
33. Lee, C., Chronis, D., Kenning, C., Peret, B., Hewezi, T., Davis, E.L., Baum, T.J., Hussey, R., Bennett, M. and Mitchum, M.G. (2011) The novel cyst nematode effector protein 19C07 interacts with the Arabidopsis auxin influx transporter LAX3 to control feeding site development. Plant Physiol. 155, 866-880.
34. Mathesius, U. (2003) Conservation and divergence of signalling pathways between roots and soil microbes-the Rhizobium-legume symbiosis compared to the development of lateral roots, mycorrhizal interactions and nematode-induced galls. Plant Soil, 255, 105-119.
35. Menges, M., Hennig, L., Gruissem, W. and Murray, J.A. (2003) Genome-wide gene expression in an Arabidopsis cell suspension. Plant Mol. Biol. 53, 423-442.
36. Mitsuda, N. and Ohme-Takagi, M. (2009) Functional analysis of transcription factors in Arabidopsis. Plant Cell Physiol. 50, 1232-1248.
37. Nemhauser, J.L., Hong, F. and Chory, J. (2006) Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell, 126, 467-475.
38. Nicol, J.M., Turner, S.J., Coyne, D.L. and Nijs, L. (2011) Current nematode threats to world agriculture. In: Genomics and Molecular Genetics of Plant-Nematode Interactions (Jones, J., Gheysen, G. and Fenoll, C., eds), pp. 21-45. Dordrecht: Springer.
39. Ogata, Y., Sakurai, N., Aoki, K., Suzuki, H., Okazaki, K., Saito, K. and Shibata, D. (2009) KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. Plant Cell Physiol. 50, 173-177.
40. Parizot, B., De Rybel, B. and Beeckman, T. (2010) VisuaLRTC: a new view on lateral root initiation by combining specific transcriptome data sets. Plant Physiol. 153, 34-40.
41. Portillo, M., Cabrera, J., Lindsey, K., Topping, J., Andrés, M.F., Emiliozzi, M., Oliveros, J.C., García-Casado, G., Solano, R., Koltai, H., Resnick, N., Fenoll, C. and Escobar, C. (2013) Distinct and conserved transcriptomic changes during nematode-induced giant cell development in tomato compared with Arabidopsis: a functional role for gene repression. New Phytol. 197, 1276-1290.
42. Puthoff, D.P., Nettleton, D., Rodermel, S.R. and Baum, T.J. (2003) Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. Plant J. 33, 911-921.
43. Riano-Pachon, D.M., Ruzicic, S., Dreyer, I. and Mueller-Roeber, B. (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics, 8, 42.
44. Sawa, S., Ohgishi, M., Goda, H., Higuchi, K., Shimada, Y., Yoshida, S. and Koshiba, T. (2002) The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis. Plant J. 32, 1011-1022.
45. Sobczak, M. and Golinowski, W. (2011) Cyst nematodes and syncytia. In: Genomics and Molecular Genetics of Plant-Nematode Interactions (Jones, J., Gheysen, G. and Fenoll, C., eds), pp. 61-82. Dordrecht: Springer.
46. Szakasits, D., Heinen, P., Wieczorek, K., Hofmann, J., Wagner, F., Kreil, D.P., Sykacek, P., Grundler, F.M. and Bohlmann, H. (2009) The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots. Plant J. 57, 771-784.
47. Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Müller, L.A., Rhee, S.Y. and Stitt, M. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37, 914-939.
48. Wieczorek, K., Golecki, B., Gerdes, L., Heinen, P., Szakasits, D., Durachko, D.M., Cosgrove, D.J., Kreil, D.P., Puzio, P.S., Bohlmann, H. and Grundler, F.M. (2006) Expansins are involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. Plant J. 48, 98-112.
49. Yang, Y., Hammes, U.Z., Taylor, C.G., Schachtman, D.P. and Nielsen, E. (2006) High-affinity auxin transport by the AUX1 influx carrier protein. Curr. Biol. 16, 1123-1127.