Comparative genomic analysis of CIPK gene family in Arabidopsis and Populus

Abstract

Calcium serves as a second messenger in various signal transduction pathways in plants. CBL-interacting protein kinases (CIP-Ks), which have a variety of functions, are involved in calcium signal transduction. Previous, the studies on CIPK family members focused on Arabidopsis and rice. Here, we present a comparative genomic analysis of the CIPK gene family in Arabidopsis and poplar, a model tree species. Twenty-seven potential CIPKs were identified from poplar using genome-wide analysis. Like the CIPK gene family from Arabidopsis, CIPK genes from poplar were also divided into intron-free and intronharboring groups. In the intron-harboring group, the intron distribution of CIPKs is rather conserved during the genome evolutionary process. Many homologous gene pairs were found in the CIPK gene family, indicating duplication events might contribute to the amplification of this gene family. The phylogenetic comparison of CIPKs in combination with intron distribution analysis revealed that CIPK genes from both Arabidopsis and poplar might have an ancient origin, which formed earlier than the separation of these two eudicot species. Our genomic and bioinformatic analysis will provide an important foundation for further functional dissection of the CBL-CIPK signaling network in poplars.

Calcineurin B-Like family in Populus: comparative genome analysis and expression pattern under cold, drought and salt stress treatment

“…However, the transcript levels of PeCBL1 and PeCBL9 decreased at 24 h, and in converse, the levels of PeCBL3, PeCBL4, PeCBL6, and PeCBL10 increased under MgCl 2 treatment. The PeActin gene was served as expression control Plant Growth Regul (2008) 56:129-140 137 active than in Arabidopsis during the evolution of genomes, which is coincident with that in the PtCIPK family (Yu et al 2007). Moreover, our analysis indicated that there are 3 paralogous pairs in PtCBL family and more existing than in Arabidopsis.…”

Molecular cloning and functional characterization of a novel CBL-interacting protein kinase NtCIPK2 in the halophyte Nitraria tangutorum

“…Subsequent studies have demonstrated the functional conservation of the CBL-CIPK pathway in Populus (Yu et al, 2007), grape (Weinl and Kudla, 2009), sorghum (Li et al, 2010), and maize (Chen et al, 2011). Enhanced tolerance to diverse stresses has also been regularly observed in transgenic Arabidopsis because of the overexpression of CIPKs (Zhao et al, 2009;Chen et al, 2012), rice (Xiang et al, 2007), tomato Huertas et al, 2012), tobacco (Tripathi et al, 2009), and apple (Hu et al, 2012).…”

Tobacco plants ectopically expressing the Ammopiptanthus mongolicus AmCBL1 gene display enhanced tolerance to multiple abiotic stresses

“…CBL proteins have no enzymatic activity and function by interacting with and regulating a group of serine-threonine protein kinases called CBL-interacting protein kinases (CIPK) (Luan et al 2002). To date, genes encoding CBLs and CIPKs have been found in all sequenced higher plant species (Yu et al 2007;Zhang et al 2008). Genome-wide analysis has revealed ten CBL members in Arabidopsis, rice, and poplar .…”