Genome-wide identification of the CPK gene family and associated responses to calcium stress in Hemiboea subcapitata

Calcium-dependent protein kinase (CPK) gene family, which can be activated directly by Ca²⁺, plays an important role in Ca²⁺ signal transduction and stress response and is widely present in green plants. So far, the role of <i>CPK</i> gene family evolution for species in karst area is far from understanding. <i>Hemiboea subcapitata</i> (Gesneriaceae) was used to explore this issue, for its mainly distributing in the karst area of south China. Our results indicated that 32 highly conserved <i>CPK</i> genes identified were distributed across 14 chromosomes in <i>H. subcapitata</i>. Additionally, 10 gene pairs were generated by fragment replication. Subcellular localization analysis revealed that <i>HsCPKs</i> were mainly localized in chloroplasts and cytoplasm. This gene family experienced intron loss events, but its motif structure was highly similar. Phylogenetic analysis showed that the <i>HsCPKs</i> were divided into four subfamilies. Subfamilies I and II were under neutral selection, while subfamilies III and IV were under strongly positive selection. The <i>HsCPKs</i> showed different expressions in three vegetative organs of <i>H. subcapitata</i>. Meanwhile, the expression levels under calcium stress revealed an overall increasing trend for all <i>HsCPK</i>s examined. Cis-acting elements analysis revealed that <i>HsCPKs</i> contained hormone-responsive elements related to stress. The expansion and evolution of <i>CPK</i> gene family in <i>H. subcapitata</i> may be related to its adaptation to calcium-rich and stressed habitats. This study provides a valuable understanding for the roles of the <i>CPK</i> gene family within karst species.