The CBL and CIPK Gene Family in Grapevine (Vitis vinifera): Genome-Wide Analysis and Expression Profiles in Response to Various Abiotic Stresses

Abstract

Calcium plays a central role in regulating signal transduction pathways. Calcineurin B-like proteins (CBLs), which harbor a crucial region consisting of EF hands that capture Ca2+, interact in a specific manner with CBL-interacting protein kinases (CIPKs). This two gene families or their interacting-complex widely respond to various environment stimuli and development processes. The genome-wide annotation and specific expression patterns of CBLs and CIPKs, however, in grapevine remain unclear. In the present study, eight CBL and 20 CIPK genes were identified in grapevine genome, and divided into four and five subfamilies, respectively, based on phylogenetic analysis, and validated by gene structure and the distribution of conserved protein motifs. Four (50%) out of eight VvCBLs and eight (40%) out of 20 VvCIPKs were found to be derived from tandem duplication, and five (25%) out of 20 VvCIPKs were derived from segmental duplication, indicating that the expansion of grapevine CBL and CIPK gene families were mainly contributed by gene duplication, and all duplication events between VvCIPK genes only detected in intron poor clade. Estimating of synonymous and non-synonymous substitution rates of both gene families suggested that VvCBL genes seems more conserved than VvCIPK genes, and were derived by positive selection pressure, whereas VvCIPK genes were mainly derived by purifying selection pressure. Expressional analyses of VvCBL and VvCIPK genes based on microarray and qRT-PCR data performed diverse expression patterns of VvCBLs and VvCIPKs in response to both various abiotic stimuli and at different development stages. Furthermore, the co-expression analysis of grapevine CBLs and CIPKs suggested that CBL-CIPK complex seems to be more responsive to abiotic stimuli than during different development stages. VvCBLs may play an important and special role in regulating low temperature stress. The protein interaction analysis suggested divergent mechanisms might exist between Arabidopsis and grapevine. Our results will facilitate the future functional characterization of individual VvCBLs and VvCIPKs.

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

“…Following the identification of 26 CIPK family genes in Arabidopsis thaliana genome [9], CIPK genes in many plant species have also been identified by genome-wide analyses of their genomes. For example, there are 34 in rice (Oryza sativa) [10], 43 in maize (Zea mays) [11], 27 in poplar (Populus tremula) [12], 23 in Brassica napus [13], 52 in soybean (Glycine max) [14], 20 in Vitis vinifera [15], 34 in apple (Malus domestica) [16], and 16 CIPKs in Prunus mume [17]. These studies reported that the CIPK gene family can be classified into two groups, including an exon-rich group and exon-poor group.…”

“…These studies reported that the CIPK gene family can be classified into two groups, including an exon-rich group and exon-poor group. 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].…”

Genes involved in stress signals: the CBLs-CIPKs network in cold tolerant Solanum commersonii

“…Our results on CIPKs confirm that this gene family in plants is larger compared to CBL. Indeed, we identified 26 CIPKs in the three potato genomes analyzed, 20, 26, and 30 CIPKs were found in Vitis, Arabidopsis, and rice, respectively (Kolukisaoglu et al 2004, Kanvar et al 2014, Xi et al 2017. These findings indicate that gene duplication events, such as segmental and/or tandem duplications might play a significant role in their expansion.…”

“…Our results indicate that both CBL and CIPK genes originate from tandem duplication events. In contrast, Xi et al (2017) reported that 50 % of VvCBLs and 40 % of VvCIPKs arise by tandem duplication, and 25 % of VvCIPKs are derived from segmental duplications in V. vinifera. Our phylogenetic analysis provided evidence that variability in the number of paralogs within different potato species were present.…”

Decoding and Relay of Calcium Signals by CBL-CIPK Module in Plants

“…The availability of a large number of sequenced plant genomes has allowed analysis of the complexity, conservation and evolution of CBL and CIPK signaling network. (Kolukisaoglu et al, 2004;Yu et al, 2007;Zhang et al, 2008;Weinl and Kudla, 2009;Piao et al, 2010;Chen et al, 2011;Lyzenga et al, 2013;Zhang et al, 2014;Sun et al, 2015;Li et al, 2016;Yin et al, 2017;Xi et al, 2017;Mo et al, 2018;Mohanta et al, 2015;Niu et al, 2018). In addition, the genome sequences for algae and non-vascular plants have also enabled us to address the evolutionary aspects of this signaling network.…”