Genome-Wide Comparative in silico Analysis of Calcium Transporters of Rice and Sorghum
10.1016/S1672-0229(11)60017-X
- Author:
Goel ANSHITA
1
,
2
;
Taj GOHAR
;
Pandey DINESH
;
Gupta SANJAY
;
Kumar ANIL
Author Information
1. Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities,G.B. Pant University of Agriculture and Technology, Pantnagar 263145, India
2. Department ofBiotechnology, Uttrakhand Technical University, Dehradun 248007, India
- Keywords:
in silico comparison;
calcium transporter;
rice;
sorghum;
genomic annotation;
synteny
- From:
Genomics, Proteomics & Bioinformatics
2011;09(4):138-150
- CountryChina
- Language:Chinese
-
Abstract:
The mechanism of calcium uptake,translocation and accumulation in Poaceae has not yet been fully understood.To address this issue,we conducted genome-wide comparative in silico analysis of the calcium (Ca2+) transporter gene family of two crop species,rice and sorghum.Gene annotation,identification of upstream cis-acting elements,phylogenetic tree construction and syntenic mapping of the gene family were performed using several bioinformatics tools.A total of 31 Ca2+ transporters,distributed on 9 out of 12 chromosomes,were predicted from rice genorne,while 28 Ca2+ transporters predicted from sorghum are distributed on all the chromosomes except chromosome 10 (Chr 10).Interestingly,most of the genes on Chr 1 and Chr 3 show an inverse syntenic relationship between rice and sorghum.Multiple sequence alignment and motif analysis of these transporter proteins revealed high conservation between the two species.Phylogenetic tree could very well identify the subclasses of channels,ATPases and exchangers among the gene family.The in silico cis-regulatory element analysis suggested diverse functions associated with light,stress and hormone responsiveness as well as endosperm- and meristem-specific gene expression.Further experiments are warranted to validate the in silico analysis of the predicted transporter gene family and elucidate the functions of Ca2+ transporters in various biological processes.
