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Background  The Ca 2+ /Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K + -dependent and K + -indendent Na + /Ca 2+  exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily.    Findings  Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H + /Cation exchanger (CAX) and cation/Ca 2+  exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg 2+ /H +  exchanger (MHX) and CAX-related Na + /Ca 2+  exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types.    Conclusions  Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0075-8) contains supplementary material, which is available to authorized users.

rice

Phylogenetic analysis and protein structure modelling identifies distinct Ca2+/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species