biologia plantarum

International journal on Plant Life established by Bohumil Němec in 1959

Biologia plantarum 60:48-54, 2016 | DOI: 10.1007/s10535-015-0565-3

Generation and characterization of expressed sequence tags in young roots of tea (Camellia assamica)

A. Das1,2, M. Mukhopadhyay1,3, T. K. Mondal1,4,*
1 Faculty of Horticulture, Uttar Banga Krishi Viswavidyalaya, Pundibari, Cooch Behar, India
2 Gauhati University, Institute of Science and Technology, Gopinath Bordoloi Nagar, Guwahati, India
3 Department of Botany, University of Kalyani, Kalyani, Nadia, India
4 Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, India

Assam tea (Camellia assamica) is perennial crop susceptible to moisture stress. We used its tender roots to construct a cDNA library for the identification, functional annotation, and analysis of transcripts. A total of 811 full-length expressed sequence tags were generated. After processing and assembly, 207 unigenes comprising 58 contigs and 149 singletons were registered. Finally, 35.75 % of the unigenes could be assigned to functional categories based on the Arabidopsis proteome. There was 43 % of a coding GC content and 1 272 coding DNA sequences found in the unigenes. Codon usage analysis shows leucine as the highest (9.92 %) and tryptophan (2.0 %) as the lowest coded amino acids. Further, a comparative study with drought-induced genes of young roots (reported earlier) reveals that 4.83 % of genes required for normal growth of roots were also induced by a drought stress. Expressions of 10 unigenes under different abiotic stresses, such as drought, cold, and salinity, were further confirmed by RT-qPCR. The sequence tags generated in this study will be valuable resources for functional genomics study of tea and other woody crop plants in future.

Keywords: cDNA library; contigs; gene expression; unigenes
Subjects: expressed sequence tags; gene expression; contigs; unigenes; tea

Received: March 6, 2015; Revised: July 1, 2015; Accepted: July 27, 2015; Published: January 1, 2016  Show citation

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Das, A., Mukhopadhyay, M., & Mondal, T.K. (2016). Generation and characterization of expressed sequence tags in young roots of tea (Camellia assamica). Biologia plantarum, 60(1), 48-54. doi: 10.1007/s10535-015-0565-3
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    References

    1. Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R., Venter, J.C.: Complementary DNA sequencing: expressed sequence tags and human genome project. - Science 252; 1651-1656, 1991. Go to original source...
    2. Borthakur, S., Mondal, T.K., Borthakur, A., Deka, P.C.; Variation in peroxidase and esterase isoenzymes in tea leaves. - Two and a Bud 42: 20-23, 1995.
    3. Chaves, M.M., Maroco, J.P., Pereira, J.S.: Understanding plant responses to drought: from genes to the whole plant. - Funct. Plant Biol. 30: 239-264, 2003. Go to original source...
    4. Chen, L., Zhao, L.P., Gao, Q.K.: Generation and analysis of expressed sequence tags from tender shoot cDNA library of tea plant (Camellia sinensis). - Plant Sci. 168: 359-363, 2005. Go to original source...
    5. Chung, E., Cho, C.W., So, H.A., Kang, J.S., Chung, Y.S., Lee, J.H.: Overexpression of VrUBC1, a mung bean E2 ubiquitin-conjugating enzyme, enhances osmotic stress tolerance in Arabidopsis. - PLoS ONE 8: e66056, 2013. Go to original source...
    6. Das, A., Das, S., Mondal, T.K.: Identification of differentially expressed gene profiles in young roots of tea [Camellia sinensis (L.) O. Kuntze] subjected to drought stress using suppression subtractive hybridization. - Plant mol. Biol. Rep. 30: 1088-1101, 2012. Go to original source...
    7. Das, A., Saha, D., Mondal, T.K.: An optimized method for extraction of RNA from tea roots for functional genomics analysis. - Indian J. Biotechnol. 12: 129-132, 2012.
    8. Deka, A., Deka, P.C., Mondal, T.K.: Tea. - In: Parthasarathy, V.A., Chattopadhyay, P.K., Bose, T.K. (ed.): Plantation Crops. Pp. 1-147. Naya Udyog, Kolkata 2006.
    9. Du, Z.Y., Chen, M.X., Chen, Q.F., Xiao, S., Chye, M.L.; Arabidopsis acyl-CoA-binding protein ACBP1 participates in the regulation of seed germination and seedling development. - Plant J. 74: 294-309, 2013. Go to original source...
    10. Huang, Y.W., Tsay, W.S., Chen, C.C., Lin, C.W., Huang, H.J.; Increased expression of the rice C-type cyclin-dependent protein kinase gene, Orysa; CDKC; 1, in response to salt stress. - Plant Physiol. Biochem. 46: 71-81, 2008. Go to original source...
    11. Konwar, B.K.: Evaluation and development of planting material. - In: Goswami, B.K. (ed.): Notes on Tea Management. Pp. 1-6. Tea Research Association, Assam 2004.
    12. Kumar, G., Kushwaha, H.R., Panjabi-Sabharwal, V., Kumari, S., Joshi, R., Karan, R., Mittal, S., Pareek, S.L., Pareek, A.; Clustered metallothionein genes are co-regulated in rice and ectopic expression of OsMT1e-P confers multiple abiotic stress tolerance in tobacco via ROS scavenging. - BMC Plant Biol. 12: 107, 2012. Go to original source...
    13. Lal, S., Gulyani, V., Khurana, P.: Overexpression of HVA1 gene from barley generates tolerance to salinity and water stress in transgenic mulberry (Morus indica). - Transgenic Res. 7; 651-663, 2008. Go to original source...
    14. Lu, S., Bahn, S.C., Qu, G., Qin, H., Hong, Y., Xu, Q., Zhou, Y., Hong, Y., Wang, X.: Increased expression of phospholipase Dα1 in guard cells decreases water loss with improved seed production under drought in Brassica napus. - Plant Biotechnol. J. 11: 380-389, 2013. Go to original source...
    15. Megdiche, W., Passaquet, C., Zourrig, W, Zuily, F.Y., Abdelly, C.: Molecular cloning and characterization of novel cystatin gene in leaves Cakile maritime, halophyte. - J. Plant Physiol. 166: 739-749, 2009. Go to original source...
    16. Mekhedov, S., Martinez, O., Ohlrogge, J.: Towards a functional catalogue of the plant genome: a survey of genes for lipid biosynthesis. - Plant Physiol. 122: 389-401, 2000. Go to original source...
    17. Mondal, T.K.: Camellia biotechnology: a bibliographic search. - Int. J. Tea Sci. 1: 28-37, 2002.
    18. Mondal, T.K.: Micropropagation of tea (Camellia sinensis). - In Jain, S.M., Ishii, K. (ed.): Micropropagation of Woody Trees and Fruits. Pp. 671-720. Kluwer Academic Publishers, Dordrecht 2003. Go to original source...
    19. Mondal, T.K. (ed.): Breeding and Biotechnology of Tea and Wild Relatives. - Springer India, New Delhi 2014. Go to original source...
    20. Mondal, T.K., Bhattacharya, A., Sharma, M., Ahuja, P.S.; Induction of in vivo somatic embryos from tea (Camellia sinensis) cotyledons. - Curr. Sci. 81: 297-300, 2001.
    21. Mukhopadyay, M., Bantawa, P., Das, A., Sarkar, B., Ghosh, P.D., Mondal, T.K.: Changes of growth, photosynthesis and alteration of leaf antioxidative defence system of tea [Camellia sinensis (L.) O. Kuntze] seedling under aluminum stress. - Biometal 25: 1141-1154, 2012. Go to original source...
    22. Park, J., Kim, J.B., Hahn, B.S., Kim, K.H., Ha, S.H., Kim, J.B., Kim, Y.H.: EST analysis and genes involved in secondary metabolism in Camellia sinensis (tea) using suppression subtractive hybridization. - Plant Sci. 166: 953-961, 2004. Go to original source...
    23. Phukon, M., Namdev, R., Deka, D., Modi, M.K., Sen, P.; Construction of cDNA library and preliminary analysis of expressed sequence tags from tea plant [Camellia sinensis (L) O. Kuntze]. - Gene 506: 202-206, 2012. Go to original source...
    24. Sambrook, J., Fritsch, E.F., Maniatis, T. (ed.): Molecular Cloning: a Laboratory Manual. - Cold Spring Harbor Laboratory Press, Cold Spring Harbor - New York 1989.
    25. Schmittgen, T.D., Livak, K.J.: Analyzing real-time PCR data by the comparative CT method. - Natur. Protocols 3: 1101-1108, 2008. Go to original source...
    26. Shinozaki, K., Yamaguchi-Shinozaki, K.: Gene networks involved in drought stress response and tolerance. - J. exp. Bot. 58: 221-227, 2007. Go to original source...
    27. Singh, B., Chauhan, H., Khurana, J.P., Khurana, P., Singh, P.; Evidence for the role of wheat eukaryotic translation initiation factor 3 subunit g (TaeIF3g) in abiotic stress tolerance. - Gene 532: 177-185, 2013. Go to original source...
    28. Stephen, F.A., Thomas, L.M., Alejandro, A.S., Jinghui, Z., Zheng, Z., Webb, M., David, J.L.: Gapped BLAST and PSIBLAST; a new generation of protein database search programs. - Nucl. Acids Res. 25: 3389-3402, 1997. Go to original source...
    29. Thanh, T., Chi, V.T., Abdullah, M.P., Omar, H., Noroozi, M., Ky, H., Napis, S.: Construction of cDNA library and preliminary analysis of expressed sequence tags from green microalga Ankistrodesmus convolutes corda. - Mol. Biol. Rep. 38: 177-182, 2011. Go to original source...
    30. Valdés-Rodríguez, S., Guerrero-Rangel, A., Melgoza-Villagómez, C., Chagolla-López, A., Delgado-Vargas, F., Martínez-Gallardo, N., Sánchez-Hernández, C., Délano-Frier, J.: Cloning of a cDNA encoding a cystatin from grain amaranth (Amaranthus hypochondriacus) showing a tissuespecific expression that is modified by germination and abiotic stress. - Plant Physiol. Biochem. 45: 790-798, 2007. Go to original source...
    31. Wong, C.E., Li, Y., Whitty, B.R., Diaz-Camino, C., Akhter, S.R., Brandle, J.E., Golding, G.B., Weretilnyk, E.A., Moffatt, B.A., Griffith, M.: Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. - Plant mol. Biol. 58: 561-574, 2005. Go to original source...
    32. Xu, D., Duan, X., Wang, B., Hong, B., Ho, T., Wu, R.; Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenic rice. - Plant Physiol. 110: 249-257, 1996. Go to original source...
    33. Yadav, R.K., Barbi, F., Ziller, A., Luis, P., Marmeisse, R., Reddy, M.S., Fraissinet-Tachet, L.: Construction of sized eukaryotic cDNA libraries using low input of total environmental meta transcriptomic RNA. - BMC Biotech. 14: 80-90, 2014. Go to original source...
    34. Yamamoto, K., Sasaki, T.: Large-scale EST sequencing in rice. - Plant mol. Biol. 35: 135-144, 1997. Go to original source...
    35. Zhou, G.A., Chang, R.Z., Qiu, L.J.: Over expression of soybean ubiquitin-conjugating enzyme gene GmUBC2 confers enhanced drought and salt tolerance through modulating abiotic stress-responsive gene expression in Arabidopsis. - Plant mol. Biol. 72: 357-67, 2010. Go to original source...

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