Genome Wide Identification, Classification and Functional Characterization of IQD Gene Family in Diploid and Tetraploid Cotton (Gossypium)

Abstract AimsCalmodulin (CaM) is considered as the most significant Ca+ signaling messenger that mediate various biochemical and physiological reactions. Whereas the calcium level can by provoked by extracellular or intracellular stimuli. CaM is activated by calcium binding proteins (CaMBPs) to regulate physiology of the cell. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. MethodsHerein, we accomplished a genome wide comparison and analysis of IQD gene family with in two diploid and tetraploid cotton species. Conserved motifs, gene structure, chromosomal map, evolutionary tree, Ka/Ks distribution, promotor analysis, venn diagram for orthologues genes, and collinearity analysis within genome and between genomes of IQD gene family in four cotton species were performed first time. Expression analysis was performed in four species of cotton from SRA database of NCBI.Results293 nonredundant IQD genes were identified from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) and clustered in the reference genomes from cotton functional genomics database. 50, 50, 94, and 99 IQD genes were detected from G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. IQD gene family in four species of cotton elucidated the role of allopolyploid and hybridization during evolutionary cascade of allotetraploid cotton. Comparatively, existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. Expression analysis revealed that GarIQD18, GarIQD25 and GarIQD50 exhibited up regulated expression trend in ovule and fiber in G. arboreum. GarIQD25 also exhibited high expression in stem, root and flower. In G. raimondii, GraIQD03 demonstrated upregulation expression across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements which are involved in plant defense and stress response mechanisms. ConclusionsOverwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD genes in improving abiotic stress tolerance in cotton.