title: Genome-wide comparative in silico analysis of calcium transporters of rice and sorghum.
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 (Ca(2+)) 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 Ca(2+) transporters, distributed on 9 out of 12 chromosomes, were predicted from rice genome, while 28 Ca(2+) 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 Ca(2+) transporters in various biological processes.
authors.affiliation: Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar 263145, India.
authors.forename: Anshita
authors.initials: A
authors.lastname: Goel
authors.forename: Gohar
authors.initials: G
authors.lastname: Taj
authors.forename: Dinesh
authors.initials: D
authors.lastname: Pandey
authors.forename: Sanjay
authors.initials: S
authors.lastname: Gupta
authors.forename: Anil
authors.initials: A
authors.lastname: Kumar
mesh_terms: D002118:Calcium / Q000378:metabolism*; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D023061:Gene Order; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D045868:Sorghum / Q000145:classification / Q000235:genetics*; D026801:Synteny
chemical_list: D010940:Plant Proteins; D002118:Calcium