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Journal of Plant Biochemistry and Biotechnology

, Volume 28, Issue 4, pp 447–459 | Cite as

Functional annotation and characterization of hypothetical protein involved in blister blight tolerance in tea (Camellia sinensis (L) O. Kuntze)

  • Gagandeep Singh
  • Gopal Singh
  • Romit Seth
  • Rajni Parmar
  • Pradeep Singh
  • Vikram Singh
  • Sanjay Kumar
  • Ram Kumar SharmaEmail author
Original Article
  • 224 Downloads

Abstract

Tea [Camellia sinensis (L) O. Kuntze], worldwide known source of popular non-alcoholic beverage, is severely affected by various biotic and abiotic stresses. Among these, blister blight (BB) disease caused by the obligate biotrophic fungus Exobasidium vexan is responsible for significant depletion of its yield and quality. Our comparative NGS transcriptomic analysis although elucidated global gene expression pattern of BB defense transitions, yet left with 12,022 transcripts categorized as ‘hypothetical proteins (HPs)’. In this study, efforts were made for assigning functions to HPs derived from RNA-Seq data and successfully identified novel putative candidates involved in BB defense in tea. Domain and family-based characterization identified 9390 HPs representing 2867 protein families and 953 super families. Of these, 213 HPs were assigned with novel putative defense related functional categories (LRR, WRKY, NAC, chitinases and peroxidases). Further, sub-cellular localization (cytosolic,133 HPs; transmembranic, 80 HPs) with abundance of HPs exhibiting of acidic (133) and basic (80) nature suggests their wider functional range. 36 HPs upregulated in tolerant genotype having significant interactions with defense responsive candidates in Protein–Protein Interaction Network analysis, possibly suggests their key regulatory role in BB defense. Interestingly, 12 stereo-dynamically stable structures [LRR (5), NAC (4), WRKY, Chitinase & Peroxidase (1 each)] of HP’s were successfully modelled based on their conserved signature sequences and empirically validated using qRT-PCR analysis, therefore, can be potential novel candidates possibly involved in signal transduction and pathogen recognition during BB defense in tea. Futuristically, novel genes identified in this study can be potentially utilized to expedite genetic improvement efforts in tea. The approach successfully employed in tea can also be adopted for assigning molecular function to the HPs in other plant species.

Keywords

Blister blight Hypothetical proteins In-silico Structural modelling Tea Transcriptome 

Abbreviations

DGE

Differential gene expression

GO

Gene ontology

HPs

Hypothetical proteins

KEGG

Kyoto encyclopedia of genes and genomes

NGS

Next generation sequencing

PPIN

Protein–protein interaction network

qRT-PCR

Quantitative real-time PCR

TF

Transcription factor

Notes

Acknowledgements

The financial support provided by Council of Scientific and Industrial Research (CSIR), New Delhi Research Grants (BSC 0301, MLP-0146), and DST grant in the form of Indo-Sri Lanka joint Research project is acknowledged. This is CSIR-IHBT Publication No. 4190.

Author contributions

GDS, RKS: Conceived and designed the experiments; GDS, GS, RS, RP: Performed the experiments; GDS, PS: Analyzed the data; GDS, GS, RS: wrote the paper; VS, SK: Helped in manuscript editing; RKS: Overall editing and approval of final version of manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.Biotechnology DepartmentCouncil of Scientific & Industrial Research-Institute of Himalayan Bioresource TechnologyPalampurIndia
  2. 2.Centre for Computational Biology and Bioinformatics, Central University of Himachal PradeshDharamshalaIndia

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