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Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.)

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Abstract

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

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Acknowledgments

The financial support by Department of Science and Technology, Government of India, New Delhi in the form of Women Scientist-A fellowship (SR/WOS-A/LS-110/2012(G) to N. Malviya is thankfully acknowledged. S. Gupta acknowledges the CSIR, New Delhi for Senior Research Fellowship. The author wishes to acknowledge the Head, Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, INDIA for infrastructural support.

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Authors and Affiliations

  1. Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, 273 009, Uttar Pradesh, India

    N. Malviya, S. Gupta & D. Yadav

  2. Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, 221 005, Uttar Pradesh, India

    V. K. Singh

  3. Department of Biotechnology, SVP University of Agriculture& Technology, Meerut, 250 110, Uttar Pradesh, India

    M. K. Yadav

  4. National Institute of Plant Genome Research JNU Campus, New Delhi, 110 067, India

    N. C. Bisht

  5. Environmental Biotechnology Division, National Environmental Engineering Research Institute- CSIR, Nehru Marg, Nagpur, 440 020, India

    B. K. Sarangi

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Supplementary material 1 (DOCX 24 kb) Table S1. Complete list of identified cis-regulatory elements of CcDof genes of pigeonpea and their position. Table S2. Function of identified cis-regulatory elements

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Malviya, N., Gupta, S., Singh, V.K. et al. Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.). Mol Biol Rep 42, 535–552 (2015). https://doi.org/10.1007/s11033-014-3797-y

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