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Genome Wide In Silico Characterization of Dof Transcription Factor Gene Family of Sugarcane and Its Comparative Phylogenetic Analysis with Arabidopsis, Rice and Sorghum

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Abstract

A total of 25 Dof genes were retrieved from GRASSIUS grass regulatory information server. These sequences were in silico characterized for homology search, multiple sequence alignment for conserved Dof DNA binding domains, distribution of conserved motifs and phylogenetic relatedness with sorghum, rice and Arabidopsis. A highly conserved four cysteine residues associated with typical zinc finger of Dof family was observed on multiple sequence alignment of Dof domains. A highly conserved cysteine residue at positions 3 and 6 along with proline and sulfur at positions 4 and 8, respectively were observed. The phylogenetic tree of 119 Dof protein sequences of sugarcane, rice, sorghum and Arabidopsis revealed ten distinct clades with several orthologs and paralogs. The distributions of 25 conserved motifs were analyzed for Dof proteins of sugarcane. Dof proteins with closely related members in the phylogenetic tree shared common motif distribution revealing the possibility of functional similarities within the same subgroup. The motif 1 representing the conserved Dof domain of 50 amino acids was uniformly observed in all the Dof proteins of sugarcane except ScDof8 and ScDof14.

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Acknowledgments

The authors wish to acknowledge Head, Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur for providing infrastructural facilities. Shubhra Gupta acknowledges CSIR for financial assistance in form of senior research fellowship. The facilities provided by DBT-SUB-DIC, Bioinformatics Centre, School of Biotechnology, BHU, Varanasi is also thankfully acknowledged.

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

    Shubhra Gupta & Dinesh Yadav

  2. Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh, 160036, India

    Hariom Kushwaha

  3. School of Biotechnology, Banaras Hindu University, Varanasi, 221 005, Uttar Pradesh, India

    Vinay Kumar Singh

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

    Naveen Chandra Bisht

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

    Bijaya Ketan Sarangi

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Gupta, S., Kushwaha, H., Singh, V.K. et al. Genome Wide In Silico Characterization of Dof Transcription Factor Gene Family of Sugarcane and Its Comparative Phylogenetic Analysis with Arabidopsis, Rice and Sorghum. Sugar Tech 16, 372–384 (2014). https://doi.org/10.1007/s12355-013-0288-8

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