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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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Title Genome wide in silico characterization of Dof transcription factor gene family of sugarcane and its comparative phylogenetic analysis with Arabidopsis, rice and sorghum
 
Creator Gupta, Shubhra
Kushwaha, Hariom
Singh, Vinay Kumar
Bisht, Naveen C.
Sarangi, Bijaya Ketan
Yadav, Dinesh
 
Subject Sugarcane
Sorghum
Arabidopsis
Rice
Dof
In silico
Multiple sequence alignment
Phylogenetic tree
 
Description Accepted date: 30 October 2013
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.
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.
 
Date 2015-12-16T06:29:39Z
2015-12-16T06:29:39Z
2014
 
Type Article
 
Identifier Sugar Tech, 16(4): 372-384
0974-0740
http://172.16.0.77:8080/jspui/handle/123456789/411
http://link.springer.com/article/10.1007%2Fs12355-013-0288-8
10.1007/s12355-013-0288-8
 
Language en_US
 
Publisher Springer