Journal of Environmental Biology

Genome wide identification and characterization of Calcium

Dependent Protein Kinase gene family in Cajanus cajan

Dhammaprakash Pandhari Wankhede¹*, Meenu Kumari², Tambi Richa³, J. Aravind¹ and Subramani Rajkumar¹

¹ICAR-National Bureau of Plant Genetic Resources, New Delhi-110 012, India

²ICAR-IIHR, Central Horticultural Experiment Station, Aiginia, Bhubaneswar-751 019, India

³Kuroda Lab, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan

*Corresponding Author E-mail: d.wankhede@icar.gov.in

Key words

CDPK family, Expression analysis,

Hidden Markov model,

Phylogenetic analysis,

Pigeonpea

Publication Data

Paper received : 22.09.2016

Revised received : 21.10.2016

Accepted : 05.11.2016

Abstract

Aim : Calcium-dependent protein kinases (CDPKs) are Ca²⁺ binding proteins which play a crucial role in plant growth and development, various biotic and abiotic stress and hormone signal transduction pathways through Ca²⁺ signal transduction mechanism. The main objective of the present study was to identify and characterize CDPK gene family from Pigeonpea genome and assign scientific nomenclature.

Methodology: A Hidden Markov model (HMM) was built from known CDPKs of other plants and searched against Pigeonpea genome. Phylogenetic analysis of CDPKs was done using Molecular Evolutionary Genetics Analysis (MEGA) 6 program. Modeller 9.15 was used to design 3-D models of CDPK proteins following homology modeling approach. Expression of identified CDPKs was studied using CLC genomics workbench making use of transcriptome Sequence Read Archive (SRA) data.

Results: Total 23 members of CDPK gene family were identified from Pigeonpea genome and characterized. The identified CDPK family was divided into four groups on the basis of sequence similarity and phylogeny. The Pigeonpea CDPKs were named following orthologous nomenclature on the basis of Arabidopsis CDPKs. A detailed in-silico characterization of Pigeonpea CDPK was performed. The transcript level evidences of Pigeonpea CDPKs was seen in the form of Expressed Sequence Tags (ESTs). Expression analysis revealed that most of the Pigeonpea CDPKs genes were expressed in two Pigeonpea cultivars, Asha and Upas120.

Interpretation: The present study gives an insight into various structural and functional aspects of CDPK family in Pigeonpea. Further, this work is expected to facilitate more elaborative and comprehensive research on CDPKs in Pigeonpea.

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