The origin, evolution and diversification of the CPK gene family in green plants

Abstract

As core integrators of plant calcium signaling, calcium-dependent protein kinases ( CPK ) are indispensable to terrestrial colonization in green plants. Nevertheless, their evolutionary dynamics across the green plant lineage remain incompletely understood. This study performed a comprehensive phylogenomic analysis of CPK genes across 86 representative green plant species. The copy numbers of CPK genes varied substantially across green plants, ranging from 2 in Chlamydomonas reinhardtii to 83 in Glycine max . Copy numbers of CPK gene family exhibited significant expansions in certain lineages (e.g., angiosperms) during evolutionary history. Phylogenetic reconstruction revealed that CPK genes in land plants were divided into four well‑supported subfamilies, whereas those from Chlamydomonas reinhardtii formed a distinct basal clade. Tandem duplication predominantly drove copy‑number expansion within each subfamily, and whole‑genome/segmental duplication were associated with the gene expansion. Core motifs and protein structures were highly conserved across different representative plant lineages, except the length of the N‑terminal variable region. Selective pressure analysis revealed that the ω values of the four CPK subfamilies were all far below 1, which indicated that all four CPK subfamilies underwent strong purifying selection. Functional enrichment further indicated that CPK genes were mainly enriched in calcium-dependent protein kinase activity and environmental adaptation pathways. High temperatures during the evolutionary history of green plants likely facilitated the diversification of CPK subfamilies. This study provides novel evolutionary insights into the adaptive significance of CPK gene family during plant terrestrialization and diversification.