Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber

Background. The calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable. Methods. In this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR). Results. Forty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development -related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs.

Automated summary

In this study, the CsCML gene family in cucumber was identified and characterized using bioinformatic analysis. Forty-four CsCML gene members were identified and analyzed for gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny. Spatiotemporal expression analysis revealed distinct expression patterns for CsCML genes in different tissues and environmental conditions, and cis-acting element analysis showed the presence of hormone, stress, and plant growth and development-related elements in the promoter regions. These findings provide a foundation for further investigation of the physiological functions of CsCMLs.