Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The Na<jats:sup>+</jats:sup>/Ca<jats:sup>2+</jats:sup> Exchanger (NCX) protein family is a member of the Cation/Ca<jats:sup>2+</jats:sup> exchanger superfamily and its members play important roles in cellular Ca<jats:sup>2+</jats:sup> homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na<jats:sup>+</jats:sup>/Ca<jats:sup>2+</jats:sup> exchangers in plants and their role in various physiological and developmental processes. In the present study, we have identified all the NCX proteins encoded in the genomes of rice and Arabidopsis and studied their phylogeny, domain architecture and expression profiles across different tissues, at various developmental stages and under stress conditions.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Through whole genome investigation, we identified twenty-two NCX proteins encoded by fifteen genes in rice and sixteen NCX proteins encoded by thirteen genes in Arabidopsis. Based on phylogenetic reconstruction, these could be classified into five clades, members of most of which were found to possess distinct domain architecture. Expression profiling of the identified NCX genes using publicly available MPSS and microarray data showed differential expression patterns under abiotic stresses, and at various development stages. In rice, OsNCX1, OsNCX8, OsNCX9 and OsNCX15 were found to be highly expressed in all the plant parts and various developmental stages. qRT-PCR based expression analysis revealed that OsNCX3, OsNCX10 and OsNCX15 were highly induced by salt and dehydration stress. Besides, expression profiling showed differential regulation of rice NCX genes in response to calcium and EGTA. Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Together, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development. Findings of the present investigation should serve as a starting point for future studies aiming functional characterization of plant NCX family proteins.</jats:p> </jats:sec>