Phylogenetic and ion-response analyses reveal a relationship between gene expansion and functional divergence in the Ca
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Phylogenetic and ion‑response analyses reveal a relationship between gene expansion and functional divergence in the Ca2+/cation antiporter family in Angiosperms Ye Zheng1 · Lin‑Bo Wang1 · Shu‑Feng Sun1 · Shi‑Ying Liu1 · Ming‑Jia Liu1 · Juan Lin1 Received: 20 February 2020 / Accepted: 21 October 2020 © Springer Nature B.V. 2020
Abstract Key message Plant CaCA superfamily genes with higher tendency to retain after WGD are more geneexpression and function differentiated in ion-response. a2+/ Abstract Plants and animals face different environmental stresses but share conserved C a2+ signaling pathways, such as C 2+ Cation transport. The Ca /cation antiporters superfamily (CaCAs) is an ancient and widespread family of ion-coupled cation transporters found in all kingdoms of life. We analyzed the molecular evolution progress of the family through comparative genomics and phylogenetics of CaCAs genes from plants and animals, grouping these genes into several families and clades, and identified multiple gene duplication retention events, particularly in the CAX ( H+/cation exchanger), CCX (cation/Ca2+ exchanger), and NCL (Na+/Ca2+ exchanger-like) families. The tendency of duplication retention differs between families and gene clades. The gene duplication events were probably the result of whole-genome duplication (WGD) in plants and might have led to functional divergence. Tissue and ion-response expression analyses revealed that CaCAs genes with more highly differentiated expression patterns are more likely to be retained as duplicates than those with more conserved expression profiles. Phenotype of Arabidopsis thaliana mutants showed that loss of genes with a greater tendency to be retained after duplication resulted in more severe growth deficiency. CaCAs genes in salt-tolerant species tended to inherit the expression characteristics of their most recent common ancestral genes, with conservative ion-response expression. This study indicates a possible evolutionary scheme for cation transport and illustrates distinct fates and a mechanism for the evolution of gene duplicates. The increased copy numbers of genes and divergences in expression might have contributed to the divergent functions of CaCAs protein, allowing plants to cope with environmental stresses and adapt to a larger number of ecological niches. Keywords Ca2+/cation antiporters superfamily (CaCAs) · Phylogenetic analyses · Selective expansion · Expression divergence · Ion-response pattern · Functional divergence
Introduction
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11103-020-01088-7) contains supplementary material, which is available to authorized users. * Juan Lin [email protected] 1
State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China
Plants use multiple mechanisms to maintain appropriate intracellular l
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