School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550009, China.
BMC Plant Biol. 2024 Apr 17;24(1):296. doi: 10.1186/s12870-024-05004-9.
Calcium-dependent protein kinases (CPKs) are crucial for recognizing and transmitting Ca signals in plant cells, playing a vital role in growth, development, and stress response. This study aimed to identify and detect the potential roles of the CPK gene family in the amphidiploid Brassica carinata (BBCC, 2n = 34) using bioinformatics methods.
Based on the published genomic information of B. carinata, a total of 123 CPK genes were identified, comprising 70 CPK genes on the B subgenome and 53 on the C subgenome. To further investigate the homologous evolutionary relationship between B. carinata and other plants, the phylogenetic tree was constructed using CPKs in B. carinata and Arabidopsis thaliana. The phylogenetic analysis classified 123 family members into four subfamilies, where gene members within the same subfamily exhibited similar conserved motifs. Each BcaCPK member possesses a core protein kinase domain and four EF-hand domains. Most of the BcaCPK genes contain 5 to 8 introns, and these 123 BcaCPK genes are unevenly distributed across 17 chromosomes. Among these BcaCPK genes, 120 replicated gene pairs were found, whereas only 8 genes were tandem duplication, suggesting that dispersed duplication mainly drove the family amplification. The results of the Ka/Ks analysis indicated that the CPK gene family of B. carinata was primarily underwent purification selection in evolutionary selection. The promoter region of most BcaCPK genes contained various stress-related cis-acting elements. qRT-PCR analysis of 12 selected CPK genes conducted under cadmium and salt stress at various points revealed distinct expression patterns among different family members in response to different stresses. Specifically, the expression levels of BcaCPK2.B01a, BcaCPK16.B02b, and BcaCPK26.B02 were down-regulated under both stresses, whereas the expression levels of other members were significantly up-regulated under at least one stress.
This study systematically identified the BcaCPK gene family in B. carinata, which contributes to a better understanding the CPK genes in this species. The findings also serve as a reference for analyzing stress responses, particularly in relation to cadmium and salt stress in B. carinata.
钙依赖蛋白激酶（CPKs）在植物细胞中识别和传递 Ca 信号方面起着至关重要的作用，在生长、发育和应激反应中发挥着重要作用。本研究旨在利用生物信息学方法鉴定和检测多倍体油菜（BBCC，2n=34）中 CPK 基因家族的潜在作用。
基于已发表的油菜基因组信息，共鉴定出 123 个 CPK 基因，其中 B 亚基因组有 70 个 CPK 基因，C 亚基因组有 53 个。为了进一步研究油菜与其他植物之间同源进化关系，利用油菜和拟南芥中的 CPK 构建了系统发育树。系统发育分析将 123 个家族成员分为四个亚家族，其中同一亚家族的基因成员具有相似的保守基序。每个 BcaCPK 成员都具有一个核心蛋白激酶结构域和四个 EF 手结构域。大多数 BcaCPK 基因含有 5 到 8 个内含子，这 123 个 BcaCPK 基因不均匀分布在 17 条染色体上。在这些 BcaCPK 基因中，发现了 120 对复制基因对，而只有 8 个基因是串联重复，表明分散复制主要驱动了家族的扩增。Ka/Ks 分析结果表明，油菜 CPK 基因家族在进化选择中主要经历了纯化选择。大多数 BcaCPK 基因的启动子区域包含各种与应激相关的顺式作用元件。在镉和盐胁迫下对 12 个选定的 CPK 基因进行 qRT-PCR 分析，发现不同家族成员对不同胁迫的反应存在明显的表达模式。具体来说，BcaCPK2.B01a、BcaCPK16.B02b 和 BcaCPK26.B02 的表达水平在两种胁迫下均下调，而其他成员的表达水平在至少一种胁迫下显著上调。
本研究系统地鉴定了油菜中的 BcaCPK 基因家族，有助于更好地了解该物种中的 CPK 基因。研究结果还为分析胁迫反应，特别是油菜对镉和盐胁迫的反应提供了参考。
