Skip to main content
SpringerLink
Log in

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

  • Original Papers
  • Published:
Biologia Plantarum

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

ds:

double strand

EST:

expressed sequence tag

LD-PCR:

long distance polymerase chain reaction

RT-qPCR:

reverse transcription quantitative PCR

References

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mondal, T.K.: Camellia biotechnology: a bibliographic search. — Int. J. Tea Sci. 1: 28–37, 2002.

    Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Mondal, T.K. (ed.): Breeding and Biotechnology of Tea and Wild Relatives. — Springer India, New Delhi 2014.

    Book  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Sambrook, J., Fritsch, E.F., Maniatis, T. (ed.): Molecular Cloning: a Laboratory Manual. — Cold Spring Harbor Laboratory Press, Cold Spring Harbor - New York 1989.

    Google Scholar 

  • Schmittgen, T.D., Livak, K.J.: Analyzing real-time PCR data by the comparative CT method. — Natur. Protocols 3: 1101–1108, 2008.

    Article  CAS  Google Scholar 

  • Shinozaki, K., Yamaguchi-Shinozaki, K.: Gene networks involved in drought stress response and tolerance. — J. exp. Bot. 58: 221–227, 2007.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Yamamoto, K., Sasaki, T.: Large-scale EST sequencing in rice. — Plant mol. Biol. 35: 135–144, 1997.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Faculty of Horticulture, Uttar Banga Krishi Viswavidyalaya, Pundibari, Cooch Behar, 785165, West Bengal, India

    A. Das, M. Mukhopadhyay & T. K. Mondal

  2. Gauhati University, Institute of Science and Technology, Gopinath Bordoloi Nagar, Guwahati, 781014, Assam, India

    A. Das

  3. Department of Botany, University of Kalyani, Kalyani, Nadia, 741235, West Bengal, India

    M. Mukhopadhyay

  4. Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India

    T. K. Mondal

Authors
  1. A. Das
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Mukhopadhyay
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. T. K. Mondal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to T. K. Mondal.

Additional information

Acknowledgements: We thank Prof. Swapan Kumar Ghosh from Uttar Banga Krishi Viswavidyalaya for encouraging us in pursuing the work, and the Director, the Tocklai Experimental Station, Tea Research Association, Jorhat, Assam for providing us the sequencing facility. We also thank Mr. Kamal Das for his technical help. The work was funded by the Department of Biotechnology, Govt. of India, New Delhi.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10535-015-0565-3

Additional key words

Search

Navigation