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Title

Annotation of gene sequence and protein structure of brinjal EDS1

 

Authors

Soumya Sharma1, Sarika Jaiswal2, Sunil Archak3,*

 

Affiliation

1Division of Bioinformatics, IARI, Pusa Campus, New Delhi, India; 2Centre for Agricultural Bioinformatics, IASRI, Pusa Campus, New Delhi, India; 3Division of Genomic Resources, NBPGR, Pusa Campus, New Delhi, India; 

 

Email

sunil.archak@icar.gov.in;

 

Article Type

Hypothesis

 

Date

Received January 13, 2017; Revised February 4, 2017; Accepted February 4, 2017; Published March 2, 2017

 

Abstract

Enhanced Disease Susceptibility1 (EDS1) is a nucleo-cytoplasmic protein, known to be a key regulator of plant basal defense and effector-triggered immunity. Sequence of a single copy brinjal EDS1 gene (SmEDS1) was mined from draft brinjal genome assembly. The extracted sequence was found to be incomplete and polished with the help of transcriptome sequence data. Full-length SmEDS1 gene is 4.5kb long having three exons that coded for 1.8kb mRNA. SmEDS1 protein is a 602 amino acid long protein consisting of Lipase3 and EP domain regions. Predicted tertiary structure of SmEDS1 using homology modelling had a mass of 68.8kD and was made of 10 strands, 26 alpha helices, five 310 helices and 43 beta turns. Phylogenetic analysis based on protein sequence grouped the species in clades defined by botanical family suggesting that EDS1 protein has evolved through the speciation process. Phylogenetic tree based on EDS1 structures grouped Solanum species of American origin (tomato, wild tomato and potato) together but brinjal EDS1 (Asiatic origin) occupied a unique  position. In silico information generated in this study is expected to be the first step toward
cloning and expression analysis of SmEDS1 gene.

 

Keywords:

brinjal; EDS1; phylogenetic analysis; structure prediction

 

Citation

Sharma et al. Bioinformation 13(3): 54-59 (2017)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.