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Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 35 issue 1-2 (march-june 2020) : 1-9,   Doi: 10.18805/BKAP206

Plant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec

A
Aamir Khan
J
Johnson George K
R
Rahul Singh Jasrotia
U
U B Angadi
M
Mir Asif Iqbal
S
Sarika Jaiswal
A
Anil Rai
D
Dinesh Kumar
1<div style="text-align: justify;">ICAR - Indian Agricultural Statistics Research Institute, New Delhi-110012, India</div>

  • Submitted24-06-2020|

  • Accepted18-07-2020|

  • First Online 10-09-2020|

  • doi 10.18805/BKAP206

Cite article:- Khan Aamir, K George Johnson, Jasrotia Singh Rahul, Angadi B U, Iqbal Asif Mir, Jaiswal Sarika, Rai Anil, Kumar Dinesh (2020). Plant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec. Bhartiya Krishi Anusandhan Patrika. 35(1): 1-9. doi: 10.18805/BKAP206.

ABSTRACT

Small cardamom (Elettaria cardamomum), is one of the costliest spices across the globe. It is grown in limited coastal tropical countries. It is widely exported agri-produce with global turnover of > 10 billion USD. It is majorly affected by the mosaic or marble disease and hence warrants the deep study at molecular level. Till now, there is no availability of whole genome sequence along with any genomic resources. Under such cases, RNA seq approach can be a rapid and economical alternative to gather the information at genomic level. De novo transcriptome assembly was carried out using Illumina Hiseq data. Analysis revealed a total of 5317 differentially expressed genes, 2267 transcription factors, >100 pathways and 175,952 genic region putative markers. Gene regulatory network analysis was performed to see the molecular events playing role in marble disease. We report the first transcriptomic results that shows the disease mechanism mediated by perturbation in auxin homeostasis and ethylene signaling. These events lead to senescence. We also developed the web-genomic resource, SCMVTDb which houses putative molecular markers, candidate genes and transcript information. Such web resource can be used in small cardamom germplasm improvement against mosaic disease in endeavour of its increased productivity. 

REFERENCES

  1. Alves, M., Dadalto, S., Gonçalves, A., de Souza, G., Barros, V., & Fietto, L. (2014).Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses. Proteomes, 2(1), 85–106. https://doi.org/10.3390/    proteomes 2010085
  2. Anjali, N., Dharan, S. S., Nadiya, F., & Sabu, K. K. (2015). Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton. International Journal of Applied Sciences and Biotechnology, (2), 188–192. https://doi.org/10.3126/ijasbt.v    3i2.12380
  3. Anjali, N., Ganga, K. M., Nadiya, F., Shefeek, S., & Sabu, K. K. (2016). Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis. SpringerPlus, 5(1), 1560. https://    doi.org/10.1186/s40064-016-3226-x
  4. Anjali, N., Nadiya, F., Thomas, J., & Sabu, K. K. (2017). Discovery of MicroRNAs in Cardamom ( Elettaria cardamomum Maton) under Drought Stress. Dataset Papers in Science, 1–4. https://doi.org/10.1155/2017/    9507485
  5. Biju, C. N., Siljo, A., & Bhat, A. I. (2010). Survey and RT-PCR Based Detection of Cardamom mosaic virus Affecting Small Cardamom in India. Indian Journal of Virology, 21(2), 148–150. https://doi.org/10.1007/s13337-    011-0026-3
  6. Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–    2120. https://doi.org/10.1093/bioinformatics /btu170
  7. Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast 2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. https://doi.org/10.1093/    bioinformatics/bti610
  8. Daneshi-Maskooni, M., Keshavarz, S. A., Mansouri, S., Qorbani, M., Alavian, S. M., Badri-    Fariman, M., Jazayeri-Tehrani, S. A., & Sotoudeh, G. (2017). The effects of green cardamom on blood glucose indices, lipids, inflammatory factors, paraxonase-1, sirtuin-    1, and irisin in patients with nonalcoholic fatty liver disease and obesity: study protocol for a randomized controlled trial. Trials, 18(1), 260. https://doi.org/10.1186/s13063-017-    1979-3
  9. Devi, U. (2016). Production of polyclonal antibody for the detection of Cardamom mosaic virus affecting cardamom (Elettaria cardamomum Maton). International Journal of Recent Innovation in Engineering and Research, 1(3), 8–11.
  10. Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., MacManes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., … Regev, A. (2013). De novo transcript sequence reconstruction from RNA -seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494–1512. https://doi.org/10.1038/    nprot.2013.084
  11. Jacob, T., & Usha, R. (2002). Expression of Cardamom mosaic virus coat protein in Escherichia coli and its assembly into filamentous aggregates. Virus Research. https://doi.org/10.1016/    S0168-1702(02)00057-6
  12. Jiang, L., & Pan, L. J. (2012). Identification and expression of C2H2 transcription factor genes in Carica papaya under abiotic and biotic stresses. Molecular Biology Reports. https:/    /doi.org/10.1007/s11033-012-1542-y
  13. Jin, H., Axtell, M. J., Dahlbeck, D., Ekwenna, O., Zhang, S., Staskawicz, B., & Baker, B. (2002). NPK1, an MEKK1-like Mitogen-Activated Protein Kinase Kinase Kinase, Regulates Innate Immunity and Development in Plants. Developmental Cell, 3(2), 291–297. https:/    /doi.org/10.1016/S1534-5807(02)00205-8
  14. Jin, J., Tian, F., Yang, D.-C., Meng, Y.-Q., Kong, L., Luo, J., & Gao, G. (2016). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, gkw982.
  15. Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323. https://doi.org/    10.1186/1471-2105-12-323
  16. Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27 (21) 2987–2993. https://doi.org/10.1093/    bioinformatics/btr509
  17. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754–1760. https://doi.org/10.1093/bio infor matics/btp324
  18. Morsy, N. F. S. (2015). A short extraction time of high quality hydrodistilled cardamom (Elettaria cardamomum L. Maton) essential oil using ultrasound as a pretreatment. Industrial Crops and Products, 65, 287–292. https://    doi.org/10.1016/j.indcrop.2014.12.012
  19. Murugan, M., Backiyarani, S., Josephrajkumar, A., Hiremath, M. B., & Shetty, P. K. (2007). Yield of small cardamom (Elettaria cardamomum M) variety PV1 as influenced by levels of nutrients and neem cake under rain fed condition in southern Western Ghats, India. 5(1), 19–25.
  20. Nadiya, F., Anjali, N., Thomas, J., Gangaprasad, A., & Sabu, K. K. (2017). Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom). Genomics Data, 11, 102–103. https://doi.org/10.1016/j.gdata.2016.12.013
  21. Nadiya, Fasiludeen, Anjali, N., Gangaprasad, A., & Sabu, K. K. (2015). High-quality RNA extraction from small cardamom tissues rich in polysaccharides and polyphenols. Analytical Biochemistry, 485, 25–27. https://doi.org/    10.1016/j.ab.2015.05.017
  22. Reyes, T., Luukkanen, O., & Quiroz, R. (2006). Small cardamom—precious for people, harmful for mountain forests: possibilities for sustainable cultivation in the east Usambaras, Tanzania. Mountain Research and Development, 26(2), 131–137.
  23. Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. https://    doi.org/10.1093/bioinformatics/btp616
  24. Sass, L. J. (1981). Religion, Medicine, Politics and Spices. Appetite, 2(1), 7–13. https://doi.org/    10.1016/S0195-6663(81)80033-5
  25. Shannon, P. (2003). Cytoscape: A Software    Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research, 13(11), 2498–2504. https://    doi.org/10.1101/gr.1239303
  26. Thiel, T., Michalek, W., Varshney, R., & Graner, A. (2003). Exploiting EST databases for the development and characterization of gene-    derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 106(3), 411–422. https://doi.org/    10.1007/s00122-002-1031-0
  27. THOMAS, J., & BHAI, R. S. (1995). Fungal and bacterial diseases of cardamom (Elettaria cardamomum Maton) and their management. Journal of Spices and Aromatic Crops, 4(1), 24–31.
  28. Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3—new capabilities and interfaces. Nucleic Acids Research, 40(15), e115–e115. https://doi.org/10.1093/nar/gks596
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Bhartiya Krishi Anusandhan Patrika
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    Research Article

    volume 35 issue 1-2 (march-june 2020) : 1-9,   Doi: 10.18805/BKAP206

    Plant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec

    A
    Aamir Khan
    J
    Johnson George K
    R
    Rahul Singh Jasrotia
    U
    U B Angadi
    M
    Mir Asif Iqbal
    S
    Sarika Jaiswal
    A
    Anil Rai
    D
    Dinesh Kumar
    1<div style="text-align: justify;">ICAR - Indian Agricultural Statistics Research Institute, New Delhi-110012, India</div>

    • Submitted24-06-2020|

    • Accepted18-07-2020|

    • First Online 10-09-2020|

    • doi 10.18805/BKAP206

    Cite article:- Khan Aamir, K George Johnson, Jasrotia Singh Rahul, Angadi B U, Iqbal Asif Mir, Jaiswal Sarika, Rai Anil, Kumar Dinesh (2020). Plant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec. Bhartiya Krishi Anusandhan Patrika. 35(1): 1-9. doi: 10.18805/BKAP206.

    ABSTRACT

    Small cardamom (Elettaria cardamomum), is one of the costliest spices across the globe. It is grown in limited coastal tropical countries. It is widely exported agri-produce with global turnover of > 10 billion USD. It is majorly affected by the mosaic or marble disease and hence warrants the deep study at molecular level. Till now, there is no availability of whole genome sequence along with any genomic resources. Under such cases, RNA seq approach can be a rapid and economical alternative to gather the information at genomic level. De novo transcriptome assembly was carried out using Illumina Hiseq data. Analysis revealed a total of 5317 differentially expressed genes, 2267 transcription factors, >100 pathways and 175,952 genic region putative markers. Gene regulatory network analysis was performed to see the molecular events playing role in marble disease. We report the first transcriptomic results that shows the disease mechanism mediated by perturbation in auxin homeostasis and ethylene signaling. These events lead to senescence. We also developed the web-genomic resource, SCMVTDb which houses putative molecular markers, candidate genes and transcript information. Such web resource can be used in small cardamom germplasm improvement against mosaic disease in endeavour of its increased productivity. 

    REFERENCES

    1. Alves, M., Dadalto, S., Gonçalves, A., de Souza, G., Barros, V., & Fietto, L. (2014).Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses. Proteomes, 2(1), 85–106. https://doi.org/10.3390/    proteomes 2010085
    2. Anjali, N., Dharan, S. S., Nadiya, F., & Sabu, K. K. (2015). Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton. International Journal of Applied Sciences and Biotechnology, (2), 188–192. https://doi.org/10.3126/ijasbt.v    3i2.12380
    3. Anjali, N., Ganga, K. M., Nadiya, F., Shefeek, S., & Sabu, K. K. (2016). Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis. SpringerPlus, 5(1), 1560. https://    doi.org/10.1186/s40064-016-3226-x
    4. Anjali, N., Nadiya, F., Thomas, J., & Sabu, K. K. (2017). Discovery of MicroRNAs in Cardamom ( Elettaria cardamomum Maton) under Drought Stress. Dataset Papers in Science, 1–4. https://doi.org/10.1155/2017/    9507485
    5. Biju, C. N., Siljo, A., & Bhat, A. I. (2010). Survey and RT-PCR Based Detection of Cardamom mosaic virus Affecting Small Cardamom in India. Indian Journal of Virology, 21(2), 148–150. https://doi.org/10.1007/s13337-    011-0026-3
    6. Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–    2120. https://doi.org/10.1093/bioinformatics /btu170
    7. Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast 2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. https://doi.org/10.1093/    bioinformatics/bti610
    8. Daneshi-Maskooni, M., Keshavarz, S. A., Mansouri, S., Qorbani, M., Alavian, S. M., Badri-    Fariman, M., Jazayeri-Tehrani, S. A., & Sotoudeh, G. (2017). The effects of green cardamom on blood glucose indices, lipids, inflammatory factors, paraxonase-1, sirtuin-    1, and irisin in patients with nonalcoholic fatty liver disease and obesity: study protocol for a randomized controlled trial. Trials, 18(1), 260. https://doi.org/10.1186/s13063-017-    1979-3
    9. Devi, U. (2016). Production of polyclonal antibody for the detection of Cardamom mosaic virus affecting cardamom (Elettaria cardamomum Maton). International Journal of Recent Innovation in Engineering and Research, 1(3), 8–11.
    10. Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., MacManes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., … Regev, A. (2013). De novo transcript sequence reconstruction from RNA -seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494–1512. https://doi.org/10.1038/    nprot.2013.084
    11. Jacob, T., & Usha, R. (2002). Expression of Cardamom mosaic virus coat protein in Escherichia coli and its assembly into filamentous aggregates. Virus Research. https://doi.org/10.1016/    S0168-1702(02)00057-6
    12. Jiang, L., & Pan, L. J. (2012). Identification and expression of C2H2 transcription factor genes in Carica papaya under abiotic and biotic stresses. Molecular Biology Reports. https:/    /doi.org/10.1007/s11033-012-1542-y
    13. Jin, H., Axtell, M. J., Dahlbeck, D., Ekwenna, O., Zhang, S., Staskawicz, B., & Baker, B. (2002). NPK1, an MEKK1-like Mitogen-Activated Protein Kinase Kinase Kinase, Regulates Innate Immunity and Development in Plants. Developmental Cell, 3(2), 291–297. https:/    /doi.org/10.1016/S1534-5807(02)00205-8
    14. Jin, J., Tian, F., Yang, D.-C., Meng, Y.-Q., Kong, L., Luo, J., & Gao, G. (2016). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, gkw982.
    15. Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323. https://doi.org/    10.1186/1471-2105-12-323
    16. Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27 (21) 2987–2993. https://doi.org/10.1093/    bioinformatics/btr509
    17. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754–1760. https://doi.org/10.1093/bio infor matics/btp324
    18. Morsy, N. F. S. (2015). A short extraction time of high quality hydrodistilled cardamom (Elettaria cardamomum L. Maton) essential oil using ultrasound as a pretreatment. Industrial Crops and Products, 65, 287–292. https://    doi.org/10.1016/j.indcrop.2014.12.012
    19. Murugan, M., Backiyarani, S., Josephrajkumar, A., Hiremath, M. B., & Shetty, P. K. (2007). Yield of small cardamom (Elettaria cardamomum M) variety PV1 as influenced by levels of nutrients and neem cake under rain fed condition in southern Western Ghats, India. 5(1), 19–25.
    20. Nadiya, F., Anjali, N., Thomas, J., Gangaprasad, A., & Sabu, K. K. (2017). Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom). Genomics Data, 11, 102–103. https://doi.org/10.1016/j.gdata.2016.12.013
    21. Nadiya, Fasiludeen, Anjali, N., Gangaprasad, A., & Sabu, K. K. (2015). High-quality RNA extraction from small cardamom tissues rich in polysaccharides and polyphenols. Analytical Biochemistry, 485, 25–27. https://doi.org/    10.1016/j.ab.2015.05.017
    22. Reyes, T., Luukkanen, O., & Quiroz, R. (2006). Small cardamom—precious for people, harmful for mountain forests: possibilities for sustainable cultivation in the east Usambaras, Tanzania. Mountain Research and Development, 26(2), 131–137.
    23. Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. https://    doi.org/10.1093/bioinformatics/btp616
    24. Sass, L. J. (1981). Religion, Medicine, Politics and Spices. Appetite, 2(1), 7–13. https://doi.org/    10.1016/S0195-6663(81)80033-5
    25. Shannon, P. (2003). Cytoscape: A Software    Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research, 13(11), 2498–2504. https://    doi.org/10.1101/gr.1239303
    26. Thiel, T., Michalek, W., Varshney, R., & Graner, A. (2003). Exploiting EST databases for the development and characterization of gene-    derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 106(3), 411–422. https://doi.org/    10.1007/s00122-002-1031-0
    27. THOMAS, J., & BHAI, R. S. (1995). Fungal and bacterial diseases of cardamom (Elettaria cardamomum Maton) and their management. Journal of Spices and Aromatic Crops, 4(1), 24–31.
    28. Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3—new capabilities and interfaces. Nucleic Acids Research, 40(15), e115–e115. https://doi.org/10.1093/nar/gks596
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