Genome-wide investigation of CIPK gene family in Aeluropus littoralis L.

The CBL-CIPK signaling network, which decodes calcium signals triggered by environmental stresses, is one of the most crucial signal transduction systems in plants. Proteins bound to calcium ions serve as sensor molecules, receiving cellular calcium ion signals and transmitting messages to the downstream gene cascade. Because of its tolerance to abiotic stresses, especially salinity stress, and its relationship to cereals, many researchers are interested in the molecular mechanisms of the halophyte grass Aeluropus littoralis. The in-silico discovery of the AlCIPK gene family and their expression profile in responses to salinity stress were considered in this analysis due to this plant's genome sequence's availability.

Using local TblastN program, the CIPK protein sequences of Arabidopsis thaliana gene families were blasted against A. littoralis genomic sequences. BlastP was used to verify all sequences after redundant sequences were removed. The detected proteins were analyzed in various protein domain databases such as Pfam, PROSITE, and InterProScan to identify, annotate, and interpret domain structures. In all of AlCIPK, the SALAD approach was used to perform similarity clustering based on motifs patterns. The exon and intron arrangement were determined by comparing the predicted CDS against AlCIPK genomic sequences in the gene structure display server (GSDS). Expasy-Prosite was used to determine the domain structure. A signal-dependent software based on SignalP 5.0 was used to identify signal peptides in proteins. Exploring the expression pattern of AtCIPK genes at various growth and developmental stages using Genevestigator (https://www.genevestigator.com/gv/plant.jsp) and the EFP browser (http://bar.utoronto.ca/). Transcriptome research was used to examine the expression patterns of AlCIPK genes in leaf and root tissues under salinity stress and recovery conditions.

Based on sequence homology with Arabidopsis genes, 20 CIPK genes were discovered in the A. littoralis genome. The Arabidopsis AtCIPK homologous proteins were used to name the Aeluropus CIPK genes. According to subcellular localization analysis, these proteins are active in a specific cellular compartment. The phylogenetic tree of 20 AlCIPK, 26 AtCIPK, and 33 OsCIPK showed that these 79 CIPKs are closely related. Exon/intron structure analysis was used to separate all AlCIPK into intron-poor and intron-rich classes. The expression of 25 AtCBL gene family members in 68 samples under salinity stress was compared using Genevestigator tools, which revealed that all 25 genes tested in different developmental/ environmental stages, including control and stress, had different expression patterns. A tissue-specific expression pattern was discovered after analyzing these AtCBL genes' expression pattern in both root and shoot tissues. In salinity stress and recovery conditions, the expression profile pattern of AlCIPK genes in leaf and root tissues was distinct. The distinct expression profiles of the AlCIPK gene family confirmed their functional and structural convergence.

Systematic study of members of this gene family revealed that CIPKs in Halophyte grass, i.e., A. littoralis, share main CIPK family characteristics with other monocotyledonous and dicotyledonous plants, which are likely important factors in this species' adaptation and stress tolerance. The lack of homologous AtCIPK24 genes in the Aeluropus genome is a key finding in this study, suggesting that the CBL-CIPK gene network in this plant has a distinct regulatory function, necessitating further studies. Future studies using the RT-qPCR method to examine the expression of AlCBL and AlCIPK gene family genes under different abiotic stresses could aid in understanding the mechanism of SOS-related gene expression regulation. This study's findings reveal the functional characteristics of the calcium gene family and provide essential information for future research on their functional roles.