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As a second messenger,calcium participates in a large number of processes of abiotic stresses and plays an important role in the process of response to adversity signaling process in cells.Calcium transmits signals to downstream through the combination with protein phosphatase B subunit like protein and calcineurin B-like protein-interacting protein kinase(CIPK)plays a key regulatory role in the growth.development and adversity of plants.At present,the research on the CIPK gene family mainly focused on the model plants such as Arabidopsis thaliana and rice,but the reports of the CIPK gene family in cotton were few.In the present study,the identification of the CIPK gene family was carried out on the whole genomes of diploid cotton(Gossypium raimondii L.)and Asian cotton Shixiya Ⅰ(Gossypium arboreum L.),and bioinformatics analysis such as gene structure was conducted on the identified CIPK gene family members to study the phylogenetic relationship and analyze the transcript expression of the CIPK gene family in different tissues in different periods.The results demonstrated that the CIPK gene family was unevenly distributed whether in the cotton D genome chromosome or A genome chromosome.A total of 41 CIPK genes were identified in the D genome of the Gossypium raimondii.mainly distributed in chromosome 10 and chromosome 9 but not chromosome 2 or chromosome 12; A total of 39 CIPK genes were identified in the A2 genome of the diploid Gossypium arboreum L.,mainly distributed in chromosome 8 and chromosome 11 but not chromosome 2 or chromosome 3.The CIPK gene family in cotton can be classified into two types according to the structures of the genes,the intron rich type and intronless type(or rare intron type),which are similar to those of the CIPK gene families of Arabidopsis thaliana,maize,rice and other plants.Phylogenetic analysis revealed that the CIPK gene family members in cotton had high evolutionary relationships with those of the dicotyledon Arabidopsis thaliana and poplar.and low evolutionary relationships with those of the monocotyledon maize and rice.The transcriptome sequencing data was employed to detect the transcription and expression of the CIPK gene family members in the leaves of the initial flowering stage and the ovule of 0 day after flowering(Day post anthesis,DPA)and 3 days after flowering.The results demonstrated that there were about 4 CIPK genes(accounting for 9.76%)of the D genome expressed in the leaves of Gossypium raimondii L..A total of 9 CIPK genes expressed in the ovule of o DPA.The ovule of 3 DPA had 11 highly expressed CIPK genes.Compared with that of the ovule of o DPA,7 CIPK genes were up-regulated in the ovule of 3 DPA.About 16 CIPK genes expressed in the genome A of the leaves of Gossypium arboreum L..There were 14 CIPK genes expressed in the ovule of 0 DPA.In comparison,13 CIPK genes expressed in the ovule of 3 DPA.Compared with that of the ovule of 0 DPA,only GaCIPK2 of the CIPK genes were significantly up-regulated in the ovule of 3 DPA.The expressions of 9 CIPK genes in the ovule of 0 DPA were similar to those of the ovule of 3 DPA,indicating that the expression of the CIPK gene family members in cotton has spatio-temporal specificity.Bioinformatics analysis and the experimental results in the present investigation lay a foundation for further research of the functions of CIPK genes of genome in cotton and lay a theoretical foundation for further research of the CBL-CIPK signaling network in cotton.