Abstract

BackgroundThe caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellular and biological processes coupled closely to the synthesis, degradation, or stability of oil bodies. Although previous studies of this protein family have been reported for Arabidopsis and other species, understanding of the evolution of the caleosin gene family in plants remains inadequate.ResultsIn this study, comparative genomic analysis was performed to investigate the phylogenetic relationships, evolutionary history, functional divergence, positive selection, and coevolution of caleosins. First, 84 caleosin genes were identified from five main lineages that included 15 species. Phylogenetic analysis placed these caleosins into five distinct subfamilies (sub I–V), including two subfamilies that have not been previously identified. Among these subfamilies, sub II coincided with the distinct P-caleosin isoform recently identified in the pollen oil bodies of lily; caleosin genes from the same lineage tended to be clustered together in the phylogenetic tree. A special motif was determined to be related with the classification of caleosins, which may have resulted from a deletion in sub I and sub III occurring after the evolutionary divergence of monocot and dicot species. Additionally, several segmentally and tandem-duplicated gene pairs were identified from seven species, and further analysis revealed that caleosins of different species did not share a common expansion model. The ages of each pair of duplications were calculated, and most were consistent with the time of genome-wide duplication events in each species. Functional divergence analysis showed that changes in functional constraints have occurred between subfamilies I/IV, II/IV, and II/V, and some critical amino acid sites were identified during the functional divergence. Additional analyses revealed that caleosins were under positive selection during evolution, and seven candidate amino acid sites (70R, 74G, 88 L, 89G, 100 K, 106A, 107S) for positive selection were identified. Interestingly, the critical amino acid residues of functional divergence and positive selection were mainly located in C-terminal domain. Finally, three groups of coevolved amino acid sites were identified. Among these coevolved sites, seven from group 2 were located in the Ca2+-binding region of crucial importance.ConclusionIn this study, the evolutionary and expansion patterns of the caleosin gene family were predicted, and a series of amino acid sites relevant to their functional divergence, adaptive evolution, and coevolution were identified. These findings provide data to facilitate further functional analysis of caleosin gene families in the plant lineage.

Highlights

  • The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species

  • Identification of caleosin genes To explore the origin and evolutionary history of the caleosin gene family, we identified caleosin genes from 15 species representing the five major plant lineages: the green algae Chlamydomonas reinhardtii and Volvox carteri; the moss Physcomitrella patens; the lycophyte Selaginella moellendorffii; the monocotyledonous angiosperms Brachypodium distachyon, Oryza sativa, Setaria italica, Zea mays, and Sorghum bicolor; and the dicotyledonous angiosperms Arabidopsis thaliana, Citrus sinensis, Glycine max, Populus trichocarpa, Brassica rapa, and Cucumis sativus

  • The analysis showed that the critical amino acid sites of functional divergence and positive selection were mainly localized in the C-terminal domain of caleosin, while coevolutionary sites were concentrated in the calcium-binding region (Figure 3)

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Summary

Introduction

The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellular and biological processes coupled closely to the synthesis, degradation, or stability of oil bodies. Lipids in plant seeds are stored in specialized organelles termed oil bodies (OBs) to serve as an energy source for germination [1]. The N-terminal hydrophilic domain of caleosin consists of an EF-hand calcium-binding motif of 28 residues including an invariable glycine residue as a structural turning point and five conserved oxygen-containing residues as calcium-binding ligands [4,10]. The C-terminal hydrophilic domain of the protein contains several potential phosphorylation sites [10,11,12]

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