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Genome-wide identification, and phylogenetic and expression profiling analyses of CaM and CML genes in Brassica rapa and Brassica oleracea

Guo, Ning, Wang, Guixiang, Zong, Mei, Han, Shuo, Liu, Fan
Gene 2018 v.677 pp. 232-244
Arabidopsis thaliana, Brassica oleracea, Brassica rapa, bromine, calcium, calcium signaling, calmodulin, diploidy, genes, phylogeny, tissues
Calmodulin (CaM) and calmodulin-like (CML) proteins are two kinds of calcium (Ca²⁺)-sensing proteins that are involved in Ca²⁺-signaling processes. B. rapa and B. oleracea are two of three diploid Brassica species that have undergone recent additional Brassiceae-lineage-specific whole-genome triplication events. To elucidate the expansion, evolution, expression pattern and interaction network of these Ca²⁺ sensors in B. rapa and B. oleracea, we conducted a comparative syntenic study on a genome-wide level using Arabidopsis thaliana. In total, 80 and 79 CaM/CML genes were identified in B. rapa and B. oleracea, respectively. The CaM/CML genes have expanded throughout the whole genomes of B. rapa and B. oleracea by whole-genome and tandem duplication events. The CaMs/CMLs of B. rapa and B. oleracea can be classified into nine subgroups based on their A. thaliana orthologs. Expression data from various tissues revealed that a large portion of CaM/CML genes exhibited patterns of differential and tissue-specific expression. The expression levels among duplicated paralogs in different subgenomes demonstrated the expression divergence of these genes in B. rapa and B. oleracea. The differential expressions of duplicated CaM and CML genes in B. rapa indicated that their functional differentiation occurred after polyploidization. The construction of interaction network and GO enrichment analysis of genes in this network revealed Br/BoCaMs/CMLs involving biological processes. This work will promote a better understanding of Ca²⁺ sensors and Ca²⁺-signaling pathways in B. rapa and B. oleracea.