Genome-wide characterization and expression profiling of GeBP gene family members in response to four abiotic stresses and ABA hormone treatment in tomato (Solanum lycopersicum L.)

In this present study, we have identified eleven GeBP genes in tomato and classified them into eight groups based on phylogenetic analysis. All eleven SlGeBP genes contain the DUF573 superfamily domain, while two additional domains FKBP_C superfamily and GT1 were predicted only in the SlGeBP2 and SlGeBP5 genes. These eleven SlGeBP genes were mapped to four different chromosomes #1,2,5,7 of tomato. Among the eleven tomato genes only one tandem duplication pair (SlGeBP3/SlGeBP4) was identified. Additionally, two segmental duplication pairs (SlGeBP11/AtGeBP11 and SlGeBP1/AtGeBP22) were identified between tomato and Arabidopsis, whereas, no duplications were observed between tomato and rice, or between rice and Arabidopsis. We also identified miRNA, hormone and stress related cis-elements as well as phosphorylation and N-glycosylation sites. Subcellular localization analysis showed that SlGeBP1, SlGeBP5, SlGeBP6 and SlGeBP7 proteins when fused with GFP were localized to the nucleus. Only SlGeBP2, SlGeBP6, SlGeBP7 and SlGeBP8 were found to be co-expressed with hub genes involved in defense, and other transcription factors in the WGCNA analysis. Organ specific expression analysis showed that GeBP1, GeBP2, GeBP3, GeBP5, GeBP6, GeBP8, GeBP9 and GeBP11 were highly upregulated in flower and fruit tissues. The remaining genes GeBP4, GeBP7 and GeBP10, were highly expressed in leaf, stem and root tissues. A single gene SlGeBP1, was upregulated in response to cold stress. Additionally, three genes SlGeBP5, SlGeBP6 and SlGeBP10 were upregulated in response to salt stress. Similarly, SlGeBP6, SlGeBP10 and SlGeBP11 were upregulated in response to drought stress. Two genes SlGeBP10 and SlGeBP11 gene were upregulated in response ABA treatment. Overall, our findings provide fundamental insights and identify potential target genes for further functional research.