Genome-wide identification and expression analysis of CIPK genes in diploid cottons

Abstract

Calcineurin B-like protein-interacting protein kinase (CIPK) plays a key regulatory role in the growth, development, and stress resistance of plants by combining with phosphatase B subunit-like protein. In the present study, CIPK genes were identified in the whole genomes of diploid cottons and their sequences were subjected to bioinformatic analyses. The results demonstrated that the CIPK gene family was unevenly distributed in two diploid cotton genomes. Forty-one CIPKs were identified in the D genome, mainly located on chromosomes 9 and 10, whereas thirty-nine CIPKs were identified in the A genome, mainly located on chromosomes 8 and 11. Based on the gene structures, CIPKs in cotton could be classified into two types: one that is intron-rich and the other that has few introns. Phylogenetic analysis revealed that the CIPK gene family members in cotton had close evolutionary relationships with those of the dicotyledonous plants, such as Arabidopsis thaliana and poplar. The analysis of transcriptome sequence data demonstrated that there were differences in gene expression in different tissues, indicating that the expression of the CIPKs in cotton had spatio-temporal specificity. The expression analysis of CIPKs under abiotic stresses (drought, salt, and low temperature) in different tissues at trefoil stage demonstrated that these stresses induced the expression of CIPKs.

Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6

“…Two genomes of allotetraploid cotton species (G. hirsutum and G. barbadense) underwent a diploidization following the divergence of G. arboreum (A genome) and G. raimondii (D genome). Based on the genome scans of two diploid cotton species, the CIPK gene family was investigated in G. raimondii (41) and G. arboreum (39) [19]. To clarify the divergence during cotton evolution, we analyzed the orthologous CIPK genes between G. raimondii, G. arboreum, and the A and D subgenomes of the two allotetraploid species (G. hirsutum and G. barbadense) (Table S5, Figure S1).…”

“…It was reported that CIPK genes participate in plant growth and development, and play critical roles in various stresses, including abiotic stresses and hormones [15,18]. The expression levels of CIPK genes in G. raimondii and G. arboreum were induced under abiotic stresses (drought, salt and low temperature) [19]. In Arabidopsis, the expression level of AtCIPK3 was enhanced during the early developmental stages of seedlings, and the Atcipk3 mutant showed high sensitivity under abscisic acid (ABA) stress during seed germination [20], and overexpression of GhCIPK6 increased tolerance to salt, drought, and ABA stresses in transgenic Arabidopsis [21].…”

“…Overexpressing the LlaCIPK gene from Lepidium can enhance cold tolerance in tobacco by increasing the level of proline and cell membrane stability [25]. Although the CIPK gene family was reported in G. arboreum and G. raimondii [19], little is known about their detailed information in G. hirsutum and G. barbadense, especially their potential roles in various abiotic stresses and cottonseed oil regulation.…”

GhCIPK6a increases salt tolerance in transgenic upland cotton by involving in ROS scavenging and MAPK signaling pathways

“…CBLs generally interact with CIPKs to form CBL-CIPK complexes that regulate downstream target proteins. CIPK proteins and CBL-CIPK complexes were involved in various responsive processes in Arabidopsis and other plants, such as rice (Oryza sativa) [26][27][28][29], maize (Zea mays) [30][31][32], Populus euphratica [33,34], canola (Brassica napus) [35,36], eggplant (Solanum melongena) [37], tomato (Solanum lycopersicum) [38], foxtail millet (Setaria italica (L.) P. Beauv) [39], pineapple (Ananas comosus) [40] and cotton [41][42][43][44]. CIPKs and CBL-CIPK complex have been implicated in the plant's response to abiotic stresses, biotic stresses, phytohormones, and nutrient deprivation [45][46][47][48][49][50].…”

GhCIPK6 Increases Salt Tolerance in Transgenic Upland Cotton by Involving in ROS Scavenging and MAPK Signaling Pathways

“…CBLs generally interact with CIPKs to form CBL-CIPK complexes that regulate downstream target proteins. CIPK proteins and CBL-CIPK complexes were involved in various responsive processes in Arabidopsis and other plants, such as rice (O. sativa) [26][27][28][29], maize (Zea mays) [30][31][32], Populus euphratica [33,34], canola (B. napus) [35,36], eggplant (Solanum melongena) [37], tomato (Solanum lycopersicum) [38], foxtail millet (Setaria italica (L.) P. Beauv) [39], pineapple (Ananas comosus) [40] and cotton [41][42][43][44]. CIPKs and CBL-CIPK complex have been implicated in the plant's response to abiotic stresses, biotic stresses, phytohormones, and nutrient deprivation [45][46][47][48][49][50].…”