Identification of RcCIPKs Gene Family in Castor Bean (Ricinus communis) and Analysis of Its Expression Pattern Under Cold Stress
WANG Xiao-Yu1,2,3,*, LIU Xu-Ming1, HAN Meng-Liang1, LI Min4, WU Yin4, JIN Ya-Nan1,2, ZHANG Ji-Xing1,2,3,*
1 College of Life Science and Food, Inner Mongolia University for Nationalities, Tongliao 028000, China; 2 Institute of Resource Biology and Ecology, College of Life Science and Food, Inner Mongolia University for Nationalities, Tongliao 028000, China; 3 Horqin Plant Stress Biology Research Institute, Inner Mongolia University for Nationalities, Tongliao 028000, China; 4 Agricultural College, Inner Mongolia University for Nationalities, Tongliao 028000, China; 5 Tianjin Agricultural University, Tianjin 300384, China
Abstract：Plants respond to the external environment by initiating a series of signaling pathways, which usually involve multiple protein kinases, such as CBL-interacting protein kinases (CIPKs). In this study, the sequence alignment method was used to identify the CIPK gene family within the whole genome of castor bean (Ricinus communis). The bioinformatics method was used to analyze the sequence structure, physical and chemical properties, chromosome positioning, cis-acting elements of promoters, conserved domains, phylogenetic relationships, and clustering methods of the encoded protein. RNA-seq and qRT-PCR were carried out to assess the expression of RcCIPKs. qRT-PCR was used to analyze the tissue-specific expression pattern of RcCIPKs and the expression level of CIPK affected by abscisic acid (ABA) hormone. The subcellular localization of RcCIPK16 were further analyzed in the epidermal cells of Nicotiana tabacum. Eighteen RcCIPKs family members were successfully identified. Gene analysis showed that RcCIPKs were divided into exon-rich and exon-poor types, which were located on 16 chromosome segments with uneven distribution. Most RcCIPKs contained MYB, MYC, ABRE and ERE elements, which indicated that these genes were responsive to plant hormone and stress. Protein analysis showed that majorities of RcCIPKs had the identical motif types and arrangement except RcCIPK3 and RcCIPK4. RcCIPKs were grouped into A, B, C, D and E categories based on phylogenetic analysis, which inferred that diverse types of CIPKs might perform various function. The results of RNA-Seq and qRT-PCR displayed that only RcCIPK1, RcCIPK12 and RcIPK16 were induced by cold stress. The tissue-specific analysis showed that RcCIPK1 and RcCIPK12 were mainly expressed in leaves and stems, and RcCIPK16 was mainly expressed in leaves; and the expression levels of the three genes were induced by ABA hormones. Subcellular localization analysis revealed that RcCIPK16 was mainly localized in the cytoplasm. This study firstly identified RcCIPKs gene family at the whole genome level and analyzed gene expression under cold stress, which will provide important candidate genes for further development of new cold tolerant castor germplasm.
王晓宇, 刘栩铭, 韩孟良, 李敏, 吴颖, 靳亚楠, 张继星. 蓖麻RcCIPKs基因家族鉴定与冷胁迫下的表达模式分析[J]. 农业生物技术学报, 2021, 29(7): 1260-1273.
WANG Xiao-Yu, LIU Xu-Ming, HAN Meng-Liang, LI Min, WU Yin, JIN Ya-Nan, , ZHANG Ji-Xing. Identification of RcCIPKs Gene Family in Castor Bean (Ricinus communis) and Analysis of Its Expression Pattern Under Cold Stress. 农业生物技术学报, 2021, 29(7): 1260-1273.
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