European Journal of Plant Pathology

, Volume 151, Issue 1, pp 173–193 | Cite as

Comparative transcriptome profiling of healthy and diseased Chowghat Green Dwarf coconut palms from root (wilt) disease hot spots

  • M. K. Rajesh
  • K. E. Rachana
  • K. Kulkarni
  • B. B. Sahu
  • R. J. Thomas
  • A. Karun


Understanding the molecular basis of host-pathogen interactions is imperative for devising disease management strategies. The root (wilt) disease is the foremost debilitating disease threatening coconut production in India. To explore the molecular mechanisms involved in compatible and incompatible interactions, global transcriptome profiling of leaves of healthy and diseased Chowghat Green Dwarf (CGD) palms was conducted. RNA-Seq analysis generated more than 190 million 100 bp reads from both healthy and diseased samples. Assembled transcriptome yielded 59,282 transcripts with a median length of 987 bp. BLASTX annotation of transcriptome resulted in 39,665 transcripts getting annotated from Uniprot and date palm proteome database. Differential gene expression profiling analysis revealed 2718 transcripts to be up- or down- regulated in the diseased palms in comparison to healthy control at a fold change of 2 and above with a p value <=0.05. The differentially expressed transcripts could be categorized into pathways which included cell wall biogenesis, primary and secondary metabolism, plant-pathogen interaction, cellular transport, hormone biosynthesis and signaling. Validation by quantitative real time PCR (RT-qPCR) of a set of arbitrarily selected genes, both up-regulated and down-regulated, established a comparable pattern as observed by RNA-Seq analysis. Overall, the resources generated in this study provide an in-depth analysis and new insights into the interaction of coconut palms with the root (wilt) disease pathogen.


Cocos nucifera Root (wilt) disease Gene expression RNA-Seq Quantitative PCR 



The authors wish to thank Indian Council of Agricultural Research (ICAR) for funding.

Author Contributions

MKR and AK conceived and designed this research. MKR, KER, RJT and AK conducted the experiments. MKR, KK, KER and BBS analyzed the data. MKR and BBS wrote the manuscript. All authors read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human studies and participants

There was no involvement of human participants and/or animals in the present study.

Informed consent

The research does not involve informed consent.

Supplementary material

10658_2017_1365_Fig9_ESM.jpg (50 kb)
Suppl. Fig. 1

Transcript length distribution in the assembled coconut leaf transcriptome (JPEG 50 kb)

10658_2017_1365_Fig10_ESM.jpg (54 kb)
Suppl. Fig. 2

a. Pie chart showing key enriched biological processes in coconut leaf transcriptome based on GO annotations obtained from date palm genome database (JPEG 54 kb)

10658_2017_1365_Fig11_ESM.jpg (45 kb)
Suppl. Fig. 2

b. Pie chart showing key enriched sub cellular localization in coconut leaf transcriptome based on GO annotations obtained from date palm genome database (JPEG 45 kb)

10658_2017_1365_Fig12_ESM.jpg (49 kb)
Suppl. Fig. 2

c. Pie chart showing key enriched molecular functions in coconut leaf transcriptome based on GO annotations obtained from date palm genome database (JPEG 49 kb)

10658_2017_1365_MOESM1_ESM.doc (52 kb)
Suppl. Table 1 (DOC 52 kb)
10658_2017_1365_MOESM2_ESM.doc (52 kb)
Suppl. Table 2 (DOC 52 kb)
10658_2017_1365_MOESM3_ESM.xls (18.9 mb)
Suppl. Table 3 List of non-redundant transcripts obtained (XLS 19390 kb)
10658_2017_1365_MOESM4_ESM.doc (36 kb)
Suppl. Table 4 (DOC 36 kb)
10658_2017_1365_MOESM5_ESM.xls (21.8 mb)
Suppl. Table 5 Annotation of coconut transcripts with date palm proteome (XLS 22372 kb)
10658_2017_1365_MOESM6_ESM.xls (64 kb)
Suppl. Table 6 Transcripts specifically expressed in diseased palms (XLS 64 kb)
10658_2017_1365_MOESM7_ESM.xls (164 kb)
Suppl. Table 7 Transcripts specifically expressed in healthy palms (XLS 163 kb)
10658_2017_1365_MOESM8_ESM.xls (578 kb)
Suppl. Table 8 Transcripts up-regulated in diseased palms (XLS 578 kb)
10658_2017_1365_MOESM9_ESM.xls (454 kb)
Suppl. Table 9 Transcripts down-regulated in diseased palms (XLS 453 kb)


  1. Abbà, S., Galetto, L., Carle, P., Carrère, S., Delledonne, M., Foissac, X., Palmano, S., Veratti, F., & Marzachì, C. (2014). RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genomics, 15(1), 1088. Scholar
  2. Afzal, A. J., Wood, A. J., & Lightfoot, D. A. (2008). Plant receptor-like serine threonine kinases: Roles in signaling and plant defense. Molecular Plant-Microbe Interactions, 21, 507–517.CrossRefPubMedGoogle Scholar
  3. Ambawat, S., Sharma, P., Yadav, N. R., & Yadav, R. C. (2013). MYB transcription factor genes as regulators for plant responses: An overview. Physiology and Molecular Biology of Plants, 19, 307–321.CrossRefPubMedCentralPubMedGoogle Scholar
  4. Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11, R106. Scholar
  5. Atkinson, N. J., & Urwin, P. E. (2012). The interaction of plant biotic and abiotic stresses: From genes to the field. Journal of Experimental Botany, 63, 3523–3543.CrossRefPubMedGoogle Scholar
  6. Bankar, K. G., Todur, V. N., Shukla, R. N., & Vasudevan, M. (2015). Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler. Genomics Data, 5, 352–359.CrossRefPubMedCentralPubMedGoogle Scholar
  7. Beliën, T., van Campenhout, S., Robben, J., & Volckaert, G. (2006). Microbial endoxylanases: Effective weapons to breach the plant cell-wall barrier or, rather, triggers of plant defense systems? Molecular Plant-Microbes Interaction, 19, 1072–1081.CrossRefGoogle Scholar
  8. Bellincampi, D., Cervone, F., & Lionetti, V. (2014). Plant cell wall dynamics and wall-related susceptibility in plant–pathogen interactions. Frontiers in Plant Science, 5, 30–37.CrossRefGoogle Scholar
  9. Berger, S., Sinha, A. K., & Roitsch, T. (2007). Plant physiology meets phytopathology: Plant primary metabolism and plant–pathogen interactions. Journal of Experimental Botany, 58, 4019–4026.CrossRefPubMedGoogle Scholar
  10. Blacklock, B. J., & Jaworski, J. G. (2006). Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases. Biochemical and Biophysical Research Communications, 346, 583–590.CrossRefPubMedGoogle Scholar
  11. Cantu, D., Vicente, A. R., Labavitch, J. M., Bennett, A. B., & Powell, A. L. (2008). Strangers in the matrix: Plant cell walls and pathogen susceptibility. Trends in Plant Science, 13, 610–617.CrossRefPubMedGoogle Scholar
  12. Chi, Y., Yang, Y., Zhou, Y., Zhou, J., Fan, B., Yu, J. Q., & Chen, Z. (2013). Protein-protein interactions in the regulation of WRKY transcription factors. Molecular Plant, 6, 287–300.CrossRefPubMedGoogle Scholar
  13. Dai, S., Zhang, Z., Bick, J., & Beachy, R. N. (2006). Essential role of the Box II cis element and cognate host factors in regulating the promoter of Rice tungro bacilliform virus. Journal of General Virology, 87, 715–722.CrossRefPubMedGoogle Scholar
  14. Dai, S., Wei, X., Alfonso, A. A., Pei, L., Duque, U. G., Zhang, Z., Babb, G. M., & Beachy, R. N. (2008). Transgenic rice plants that over express transcription factors RF2a and RF2b are tolerant to rice tungro virus replication and disease. Proceedings of the National Academy of Sciences, 105, 21012–21016.CrossRefGoogle Scholar
  15. Dao, T. T. H., Linthorst, H. J. M., & Verpoorte, R. (2011). Chalcone synthase and its functions in plant resistance. Phytochemistry Reviews, 10, 397–412.CrossRefPubMedCentralPubMedGoogle Scholar
  16. De Hoon, M. J. L., Imoto, S., Nolan, J., & Miyano, S. (2004). Open source clustering software. Bioinformatics, 20, 1453–1453.CrossRefPubMedGoogle Scholar
  17. Eynck, C., Séguin-Swartz, G., Clarke, W. E., & Parkin, I. A. P. (2012). Monolignol biosynthesis is associated with resistance to Sclerotinia sclerotiorum in Camelina sativa. Molecular Plant Pathology, 13, 887–899.CrossRefPubMedGoogle Scholar
  18. Fan, G., Dong, Y., Deng, M., Zhao, Z., Niu, S., & Xu, E. (2014). Plant-pathogen interaction, circadian rhythm, and hormone-related gene expression provide indicators of phytoplasma infection in Paulownia fortunei. International Journal of Molecular Sciences, 15(12), 23141–23162.CrossRefPubMedCentralPubMedGoogle Scholar
  19. Fan, G., Cao, X., Niu, S., Deng, M., Zhao, Z., & Dong, Y. (2015). Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa. BMC Genomics, 16(1), 896. Scholar
  20. Ferrer, J. L., Austin, M. B., Stewart, C., & Noel, J. P. (2008). Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiology and Biochemistry, 46, 356–370.CrossRefPubMedGoogle Scholar
  21. Greeff, C. C., Roux, M. M., Mundy, J. J., & Petersen, M. M. (2012). Receptor-like kinase complexes in plant innate immunity. Frontiers in Plant Science, 3, 209. Scholar
  22. Grefen, C., & Harter, K. (2004). Plant two-component systems: Principles, functions, complexity and cross talk. Planta, 219, 733–742.CrossRefPubMedGoogle Scholar
  23. Gurr, G. M., Johnson, A. C., Ash, G. J., Wilson, B. A. L., Ero, M. M., Pilotti, C. A., Dewhurst, C. F., & You, M. S. (2016). Coconut lethal yellowing diseases: A phytoplasma threat to palms of global economic and social significance. Frontiers in Plant Science, 7, 1521. Scholar
  24. Henschel, R., Nista, P. M., Lieber, M., Haas, B. J., Wu, L. S., Nista, P. M., Haas, B. J., & Le Duc, R. D. (2012). Trinity RNA-Seq assembler performance optimization. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging From the Extreme to the Campus and Beyond (pp. 1–8). ACM.Google Scholar
  25. Huang, Y. Y., Lee, C. P., Fu, J. L., Chang, B. C., Matzke, A. J., & Matzke, M. (2014). De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. G3: Genes Genomes Genetics, 4, 2147–2157.CrossRefPubMedCentralPubMedGoogle Scholar
  26. Jacob, P. M., Nair, R. V., & Rawther, T. S. S. (1998). Varietal resistance. In K. U. K. Nampoothiri & P. K. Koshy (Eds.), Coconut Root (wilt) Disease (pp. 97–104). Kasaragod: CPCRI.Google Scholar
  27. Kangasjärvi, S., Neukermans, J., Li, S., Aro, E. M., & Noctor, G. (2012). Photosynthesis, photorespiration, and light signalling in defence responses. Journal of Experimental Botany, 63, 1619–1636.CrossRefPubMedGoogle Scholar
  28. Kissoudis, C., van de Wiel, C., Visser, R. G. F., & van der Linden, G. (2014). Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk. Frontiers in Plant Science, 5, 207. Scholar
  29. Koshy, P. K. (1999). Root (wilt) disease of coconut. Indian Phytopathology, 52, 335–353.Google Scholar
  30. Kostyn, K., Czemplik, M., Kulma, A., Bortniczuk, M., Skała, J., & Szopa, J. (2012). Genes of phenylpropanoid pathway are activated in early response to Fusarium attack in flax plants. Plant Science, 190, 103–115.CrossRefPubMedGoogle Scholar
  31. Lecourieux, D., Raneva, R., & Pugin, A. (2006). Calcium in plant defence-signalling pathways. New Phytologist, 171, 249–269.CrossRefPubMedGoogle Scholar
  32. Lionetti, V., Raiola, A., Camardella, L., Giovane, A., Obel, N., Pauly, M., Favaron, F., Cervone, F., & Bellincampi, D. (2007). Overexpression of pectin methylesterase inhibitors in Arabidopsis restricts fungal infection by Botrytis cinerea. Plant Physiology, 143, 1871–1880.CrossRefPubMedCentralPubMedGoogle Scholar
  33. Lionetti, V., Cervone, F., & Bellincampi, D. (2012). Methyl esterification of pectin plays a role during plant–pathogen interactions and affects plant resistance to diseases. Journal of Plant Physiology, 169, 1623–1630.CrossRefPubMedGoogle Scholar
  34. Liu, R., Dong, Y., Fan, G., Zhao, Z., Deng, M., Cao, X., & Niu, S. (2013). Discovery of genes related to witches broom disease in Paulownia tomentosa × Paulownia fortunei by a de novo assembled transcriptome. PLoS One, 8(11), e80238. Scholar
  35. Liu, L. Y., Tseng, H. I., Lin, C. P., Lin, Y. Y., Huang, Y. H., Huang, C. K., Chang, T. H., & Lin, S. S. (2014). High-throughput transcriptome analysis of the leafy flower transition of Catharanthusroseus induced by peanut witches'-broom phytoplasma infection. Plant Cell Physiology, 55(5), 942–957.CrossRefPubMedGoogle Scholar
  36. Manimekalai, R., Soumya, V. P., Sathish Kumar, R., Selvarajan, R., Reddy, K., Thomas, G. V., Sasikala, M., Rajeev, G., & Baranwal, V. K. (2010). Molecular detection of 16SrXI group phytoplasma associated with root (wilt) disease of coconut (Cocos nucifera L.) in India. Plant Disease, 94, 636–636.CrossRefGoogle Scholar
  37. Mao, G., Meng, X., Liu, Y., Zheng, Z., Chen, Z., & Zhang, S. (2011). Phosphorylation of a WRKY transcription factor by two pathogen-responsive MAPKs drives phytoalexin biosynthesis in Arabidopsis. Plant Cell, 23, 1639–1653.CrossRefPubMedCentralPubMedGoogle Scholar
  38. Mardi, M., Karimi Farsad, L., Gharechahi, J., & Salekdeh, G. H. (2015). In-depth transcriptome sequencing of Mexican lime trees infected with Candidatus Phytoplasma aurantifolia. PLoS One, 10(7), e0130425. Scholar
  39. Martinelli, F., Uratsu, S. L., Albrecht, U., Reagan, R. L., Phu, M. L., Britton, M., Buffalo, V., Fass, J., Leicht, E., Zhao, W., & Lin, D. (2012). Transcriptome profiling of citrus fruit response to Huanglongbing disease. PLoS One, 7(5), e38039. Scholar
  40. McGrath, K. C., Dombrecht, B., Manners, J. M., Schenk, P. M., Edgar, C. I., Maclean, D. J., Scheible, W. R., Udvardi, M. K., & Kazan, K. (2005). Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiology, 139, 949–959.CrossRefPubMedCentralPubMedGoogle Scholar
  41. Moeder, W., Urquhart, W., Ung, H., & Yoshioka, K. (2011). The role of cyclic nucleotide-gated ion channels in plant immunity. Molecular Plant, 4, 442–452.CrossRefPubMedGoogle Scholar
  42. Mou, H. Q., Lu, J., Zhu, S. F., Lin, C. L., Tian, G. Z., Xu, X., & Zhao, W. J. (2013). Transcriptomic analysis of Paulownia infected by Paulownia witches’-broom Phytoplasma. PLoS One, 8, e77217. Scholar
  43. Nagalakshmi, U., Waern, K., & Snyder, M. (2010). RNA-Seq: A method for comprehensive transcriptome analysis. Current Protocols in Molecular Biology.
  44. Nair, M. K., Koshy, P. K., Jacob, P. M., Nair, R. V., Bhaskara Rao, E. V. V., Nampoothiri, K. U. K., & Iyer, R. D. (1996). A root (wilt) disease resistant coconut hybrid and strategy for resistance breeding. Indian Coconut Journal, 27, 2–5.Google Scholar
  45. Nair, R. V., Jacob, P. M., & Ajithkumar, R. (2004). Screening of coconut varieties against root (wilt) disease. Journal of Plantation Crops, 32, 50–51.Google Scholar
  46. Nambiar, P. T. N., & Pillai, N. G. (1985). A simplified method of indexing root (wilt) affected coconut palms. Journal of Plantation Crops, 13, 35–37.Google Scholar
  47. Nawrath, C., Heck, S., Parinthawong, N., & Métraux, J. P. (2002). EDS5, an essential component of salicylic acid–dependent signaling for disease resistance in Arabidopsis, is a member of the MATE transporter family. The Plant Cell, 14, 275–286.CrossRefPubMedCentralPubMedGoogle Scholar
  48. Nejat, N., Sijam, K., Abdullah, S. N. A., Vadamalai, G., & Dickinson, M. (2009). Molecular characterization of a phytoplasma associated with coconut yellow decline (CYD) in Malaysia. American Journal of Applied Sciences, 6, 1331–1340.CrossRefGoogle Scholar
  49. Nejat, N., Cahill, D. M., Vadamalai, G., Ziemann, M., Rookes, J., & Naderali, N. (2015). Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection. Molecular Genetics and Genomics, 290, 1899–1910.CrossRefPubMedGoogle Scholar
  50. Nuruzzaman, M., Sharoni, A. M., & Kikuchi, S. (2013). Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Frontiers in Microbiology, 4, 248. Scholar
  51. Osakabe, Y., Yamaguchi-Shinozaki, K., Shinozaki, K., & Tran, L. S. (2013). Sensing the environment: Key roles of membrane-localized kinases in plant perception and response to abiotic stress. Journal of Experimental Botany, 64, 445–458.CrossRefPubMedGoogle Scholar
  52. Ozsolak, F., & Milos, P. M. (2011). RNA sequencing: Advances, challenges and opportunities. Nature Reviews Genetics, 12, 87–98.CrossRefPubMedGoogle Scholar
  53. Perera, S. A. C. N., Herath, H. M. N. B., Wijesekera, H. T. R., Subhathma, W. G. R., & Weerakkody, W. A. T. L. (2015). Evaluation of coconut germplasm in Weligama and Matara area of the Southern Province of Sri Lanka for resistance to Weligama coconut leaf wilt disease. Cocos, 21, 15–20.CrossRefGoogle Scholar
  54. Petruccelli, S., Dai, S., Carcamo, R., Yin, Y., Chen, S., & Beachy, R. N. (2001). Transcription factor RF2a alters expression of the rice tungro bacilliform virus promoter in transgenic tobacco plants. Proceedings of the National Academy of Sciences, 98, 7635–7640.CrossRefGoogle Scholar
  55. Pfaffl, M. W., Horgan, G. W., & Dempfle, L. (2002). Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Research, 30, e36.CrossRefPubMedCentralPubMedGoogle Scholar
  56. Pham, J., Liu, J., Bennett, M. H., & Mansfield, J. W. (2012). Arabidopsis histidine kinase 5 regulates salt sensitivity and resistance against bacterial and fungal infection. New Phytologist, 194, 168–180.CrossRefPubMedGoogle Scholar
  57. Quaicoe, R. N., Dery, S. K., Philippe, R., Baudouin, L., Nipah, J. O., Nkansah-Poku, J., Arthur, R., Dare, D., Yankey, E. N., Pilet, F., & Dollet, M. (2009). Resistance screening trials on coconut varieties to Cape Saint Paul Wilt Disease in Ghana. Oléagineux, 16, 132–136.CrossRefGoogle Scholar
  58. Raffaele, S., Leger, A., & Roby, D. (2009). Very long chain fatty acid and lipid signaling in the response of plants to pathogens. Plant Signaling & Behavior, 4, 94–99.CrossRefGoogle Scholar
  59. Rajesh, M. K., Rachana, K. E., Fayas, T. P., Babu, M., Kiran, A. G., & Karun, A. (2014). Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in coconut. In K. Muralidharan, M. K. Rajesh, K. S. Muralikrishna, J. Vijayan, & S. Jayasekhar (Eds.), Book of Abstracts of National Seminar on Sustainability of Coconut, Arecanut and Cocoa Farming-Technological Advances and Way Forward (p. 34). Kasaragod: ICAR-CPCRI.Google Scholar
  60. Rajesh, M. K., Fayas, T. P., Naganeeswaran, S., Rachana, K. E., Bhavyashree, U., Sajini, K. K., & Karun, A. (2016). De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing. Protoplasma, 253, 913–928.CrossRefPubMedGoogle Scholar
  61. Rojas, C. M., Senthil-Kumar, M., Tzin, V., & Mysore, K. S. (2014). Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense. Frontiers in Plant Science, 5, 17. Scholar
  62. Saensuk, C., Wanchana, S., Choowongkomon, K., Wongpornchai, S., Kraithong, T., Imsabai, W., Chaichoompu, E., Ruanjaichon, V., Toojinda, T., Vanavichit, A., & Arikit, S. (2016). De novo transcriptome assembly and identification of the gene conferring a “pandan-like” aroma in coconut (Cocos nucifera L.) Plant Science, 252, 324–334.CrossRefPubMedGoogle Scholar
  63. Saldanha, A. J. (2004). Java Tree view-extensible visualization of microarray data. Bioinformatics, 20, 3246–3248.CrossRefPubMedGoogle Scholar
  64. Sanchez, F. I. J. (2008). Polyketide synthases in Cannabis sativa L. PhD thesis, Pharmacognosy Department, Section of Metabolomics, Institute of Biology, Faculty of Science, Leiden University.Google Scholar
  65. Sánchez-Rangel, D., Rivas-San Vicente, M., de la Torre-Hernández, M. E., Nájera-Martínez, M., & Plasencia, J. (2014). Deciphering the link between salicylic acid signaling and sphingolipid metabolism. Frontiers in Plant Science, 6, 125. Scholar
  66. Sasikala, M., Rajeev, G., Prakash, V. R., & Amith, S. (2010). Modified protocol of ELISA for rapid detection of coconut root (wilt) disease. Journal of Plantation Crops, 38, 16–19.Google Scholar
  67. Scheideler, M., Schlaich, N. L., Fellenberg, K., Beissbarth, T., Hauser, N. C., Vingron, M., Slusarenko, A. J., & Hoheisel, J. D. (2002). Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. Journal of Biological Chemistry, 277, 10555–10561.CrossRefPubMedGoogle Scholar
  68. Seifi, H. S., Van Bockhaven, J., Angenon, G., & Höfte, M. (2013). Glutamate metabolism in plant disease and defense: Friend or foe? Molecular Plant-Microbe Interactions, 26, 475–485.CrossRefPubMedGoogle Scholar
  69. Seifi, H. S., De Vleesschauwer, D., Aziz, A., & Höfte, M. (2014). Modulating plant primary amino acid metabolism as a necrotrophic virulence strategy: The immune-regulatory role of asparagine synthetase in Botrytis cinerea-tomato interaction. Plant Signaling & Behavior, 9, e27995.CrossRefGoogle Scholar
  70. Seo, E., & Choi, D. (2015). Functional studies of transcription factors involved in plant defenses in the genomics era. Briefings in Functional Genomics, 14, 260–267.CrossRefPubMedGoogle Scholar
  71. Seo, P. J., & Park, C. M. (2010). MYB96-mediated abscisic acid signals induce pathogen resistance response by promoting salicylic acid biosynthesis in Arabidopsis. New Phytologist, 186, 471–483.CrossRefPubMedGoogle Scholar
  72. Shiu, S. H., & Bleecker, A. B. (2001). Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences, 98, 10763–10768.CrossRefGoogle Scholar
  73. Siewert, C., Luge, T., Duduk, B., Seemüller, E., Büttner, C., Sauer, S., & Kube, M. (2014). Analysis of expressed genes of the bacterium 'Candidatus phytoplasma Mali' highlights key features of virulence and metabolism. PLoS One, 9(4), e94391. Scholar
  74. Singh, P. K., Akram, M., Vajpeyi, M., Srivastava, R. L., Kumar, K., & Naresh, R. (2007). Screening and development of resistant sesame varieties against phytoplasm. Bulletin of Insectology, 60, 303–304.Google Scholar
  75. Solomon, J. J., Govindankutty, M. P., & Nienhaus, F. (1983). Association of mycoplasma-like organisms with the coconut root (wilt) disease in India. ZeitschriftfuerPflanzenkrankheiten und Pflanzenschutz, 90, 295–297.Google Scholar
  76. Sugio, A., MacLean, A. M., Grieve, V. M., & Hogenhout, S. A. (2011). Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis. Proceedings of the National Academy of Sciences, 108, E1254–E1263.CrossRefGoogle Scholar
  77. Sun, L., Zhang, H., & Li, D. (2013). Functions of rice NAC transcriptional factors, ONAC122 and ONAC131, in defense responses against Magnaporthe grisea. Plant Molecular Biology, 81, 41–56.CrossRefPubMedGoogle Scholar
  78. Thomas, R. J., Rajesh, M. K., Jacob, P. M., Jose, M., & Nair, R. V. (2015). Studies on genetic uniformity of Chowghat Green Dwarf and Malayan Green Dwarf varieties of coconut using molecular and morphometric methods. Journal of Plantation Crops, 43, 89–96.Google Scholar
  79. Toth, Z., Winterhagen, P., Kalapos, B., Su, Y., Kovacs, L., & Kiss, E. (2016). Expression of a grapevine NAC transcription factor gene is induced in response to powdery mildew colonization in salicylic acid-independent manner. Scientific Reports, 6, 30825. Scholar
  80. Vogt, T. (2010). Phenylpropanoid biosynthesis. Molecular Plant, 3, 2–20.CrossRefPubMedGoogle Scholar
  81. Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57–63.CrossRefPubMedCentralPubMedGoogle Scholar
  82. Wang, G. Y., Shi, J. L., Ng, G., Battle, S. L., Zhang, C., & Lu, H. (2011). Circadian clock-regulated phosphate transporter PHT4;1 plays an important role in Arabidopsis defense. Molecular Plant, 4, 516–526.CrossRefPubMedCentralPubMedGoogle Scholar
  83. Wang, G., Zhang, C., Battle, S., & Lu, H. (2014). The phosphate transporter PHT4; 1 is a salicylic acid regulator likely controlled by the circadian clock protein CCA1. Frontiers in Plant Science, 5, 701. Scholar
  84. Wang, Y., Zhou, L., Yu, X., Stover, E., Luo, F., & Duan, Y. (2016). Transcriptome profiling of Huanglongbing (HLB) tolerant and susceptible citrus plants reveals the role of basal resistance in HLB tolerance. Frontiers in Plant Science.
  85. Ward, J. L., Forcat, S., Beckmann, M., Bennett, M., Miller, S. J., Baker, J. M., Hawkins, N. D., Vermeer, C. P., Lu, C., Lin, W., & Truman, W. M. (2010). The metabolic transition during disease following infection of Arabidopsis thaliana by Pseudomonas syringae pv. tomato. Plant Journal, 63, 443–457.CrossRefPubMedGoogle Scholar
  86. Willats, W. G., McCartney, L., Mackie, W., & Knox, J. P. (2001). Pectin: Cell biology and prospects for functional analysis. Plant Molecular Biology, 47, 9–27.CrossRefPubMedGoogle Scholar
  87. Yin, Y., Chen, L., & Beachy, R. (1997). Promoter elements required for phloem-specific gene expression from the RTBV promoter in rice. Plant Journal, 12, 1179–1188.CrossRefPubMedGoogle Scholar
  88. Zeier, J. (2013). New insights into the regulation of plant immunity by amino acid metabolic pathways. Plant, Cell and Environment, 36, 2085–2103.CrossRefPubMedGoogle Scholar
  89. Zhang, Q., & Xiao, S. (2015). Lipids in salicylic acid-mediated defense in plants: Focusing on the roles of phosphatidic acid and phosphatidylinositol 4-phosphate. Frontiers in Plant Science, 6, 387. Scholar
  90. Zhang, S. H., Yang, Q., & Ma, R. C. (2007). Erwinia carotovora ssp. carotovora infection induced “defense lignin” accumulation and lignin biosynthetic gene expression in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Journal of Integrative Plant Biology, 49, 993–1002.CrossRefGoogle Scholar

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© Koninklijke Nederlandse Planteziektenkundige Vereniging 2017

Authors and Affiliations

  • M. K. Rajesh
    • 1
  • K. E. Rachana
    • 1
  • K. Kulkarni
    • 2
  • B. B. Sahu
    • 3
  • R. J. Thomas
    • 4
  • A. Karun
    • 1
  1. 1.ICAR-Central Plantation Crops Research InstituteKasaragodIndia
  2. 2.Bionivid Technology Private LimitedBengaluruIndia
  3. 3.National Institute of TechnologyRourkelaIndia
  4. 4.ICAR-CPCRI (RS)KayamkulamIndia

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