In silico identification and expression analysis of Rare Cold Inducible 2 (RCI2) gene family in cucumber

Rare Cold Inducible 2 (RCI2), also known as plasma membrane protein 3, is a group of low molecular weight proteins that play crucial roles in plant growth and development as well as environmental stress responses. In this work, we performed a comprehensive analysis of the RCI2 gene family and identified 4 RCI2 genes (CsaRCI2A–D) from cucumber (Cucumis sativus L.), which were distributed in four chromosomes of the cucumber genome. The amino acid identities among the 4 CsaRCI2 proteins varied from 46.55 to 76.00%. Phylogenetic analysis showed that RCI2 proteins from cucumber, Arabidopsis, Medicago truncatula, maize and rice could be classified into four distinct clades, and nearly all the RCI2 genes harbored two exons separated by an intron of variable size. Many development-, stress-, and hormone-related cis-elements were found in the promoter regions of the CsaRCI2 genes, and the CsaRCI2 genes seemed to have tissue-specific expression patterns. In addition, qRT-PCR analysis revealed that these four CsaRCI2 genes were all responsive to various abiotic stresses including cold, salt, and drought, as well as ABA treatment. Our findings lay a foundation for further elucidating the biological roles of the RCI2 gene family in cucumber.