Genome-wide identification and characterization of CaM and CML gene family in chickpea (Cicer arietinum L.)

Calcium (Ca2+) is a ubiquitous secondary messenger that conveys a variety of internal and external signals. Sensor proteins most likely detect these Ca2+ signals and can bind Ca2+ using the EF-hand motif, a helix-loop-helix structure. Calmodulins (CaMs) and calmodulin-like proteins (CMLs) are one of the major classes of calcium (Ca2+) sensors in plants. However, knowledge about the CaM and CML families in chickpea is still missing. To fill this knowledge gap, a comprehensive analysis of CaM and CML was performed in this study, and six CaM and twenty-three CML genes in chickpea were identified. The gene structure analysis showed that twenty-one out of twenty-three CaCMLs were intron-less, whereas all the CaCaMs were rich in introns. Their chromosomal locations showed that twenty-six out of twenty-nine genes could be mapped on seven chromosomes, and three genes i.e., CaCaM3, CaCML18, and CaCML20 are placed on the scaffold region. Ka/Ks analysis of orthologous and paralogous gene pairs indicated that all the CaCaM and CaCML gene pairs evolved through purifying selection. According to phylogenetic analysis, CaCaM and CaCML proteins were clustered into five orthologous groups. Group V contains the highest number of CaM and CML protein members of chickpea. Numerous cis-acting regulatory elements associated with abiotic stress, hormone signalling, and plant growth and development were identified through promoter analysis. Box 4 cis-acting regulatory element is present in all the CaCaM and CaCML promoter sequences. By analyzing the available transcriptome data, we generated a detailed expression profile of CaCaMs and CaCMLs across different tissues, such as root, shoot, mature leaf, flower bud, and young pod, various developmental stages of flowers, and different abiotic stress conditions. The identification and description of CaCaMs and CaCMLs in chickpea provide a framework for further functional characterization of these genes. These results suggest that the CaM and CML gene family may play an important role in growth and development of chickpea under normal and stress conditions.