Insight into the CBL and CIPK gene families in pecan (Carya illinoinensis): identification, evolution and expression patterns in drought response.
Insight into the CBL and CIPK gene families in pecan (Carya illinoinensis): identification, evolution and expression patterns in drought response.
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DOI：
10.1186/s12870-022-03601-0
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发表时间：
2022-04-28
影响因子：
5.3
通讯作者：
Peng, Fangren
中科院分区：
文献类型：
--
作者：
Zhu, Kaikai;Fan, Pinghua;Liu, Hui;Tan, Pengpeng;Ma, Wenjuan;Mo, Zhenghai;Zhao, Juan;Chu, Guolin;Peng, Fangren
钙离子（Ca 2+）作为一种普遍存在的第二信使，在信号转导中起着关键作用。钙调磷酸酶B样蛋白（CBL）是植物特异性的钙离子传感器，与CBL相互作用蛋白激酶（CIPK）相互作用以传递钙离子信号。CBL-CIPK复合物在植物生长发育和干旱胁迫响应中起着重要作用，但目前关于山核桃CBL和CIPK基因的研究还很有限。本研究共从山核桃基因组中鉴定出9个CBL基因和30个CIPK基因，并根据遗传分化将其分别划分为4个和5个分支。基因结构和保守序列基序分析表明，同一进化枝的家族成员通常表现出相似的外显子-内含子结构和基序组成。片段重复事件对山核桃CBL和CIPK基因家族的扩展贡献很大，Ka/Ks值显示它们都经历了强烈的负选择。对14种植物CIPK蛋白的系统发育分析表明，CIPK基因在内含子缺失的进化枝中起源于种子植物。分析了CiCBL和CiCIPK的组织特异性表达谱，呈现功能多样性。来自RNA-Seq的表达谱揭示了山核桃干旱处理下CiCBL和CiCIPKs的不同表达模式。此外，共表达网络分析有助于阐明这些基因之间的关系，并确定潜在的候选人调节干旱反应，这是由qRT-PCR分析验证。对山核桃基因组中CBL和CIPK基因的鉴定和分析为进一步研究CiCBL和CiCIPK在山核桃干旱胁迫响应中的功能奠定了基础。在线版本包含补充材料，可通过10.1186/s12870-022-03601-0获得。
Calcium (Ca2+) serves as a ubiquitous second messenger and plays a pivotal role in signal transduction. Calcineurin B-like proteins (CBLs) are plant-specific Ca2+ sensors that interact with CBL-interacting protein kinases (CIPKs) to transmit Ca2+ signals. CBL-CIPK complexes have been reported to play pivotal roles in plant development and response to drought stress; however, limited information is available about the CBL and CIPK genes in pecan, an important nut crop. In the present study, a total of 9 CBL and 30 CIPK genes were identified from the pecan genome and divided into four and five clades based on phylogeny, respectively. Gene structure and distribution of conserved sequence motif analysis suggested that family members in the same clade commonly exhibited similar exon-intron structures and motif compositions. The segmental duplication events contributed largely to the expansion of pecan CBL and CIPK gene families, and Ka/Ks values revealed that all of them experienced strong negative selection. Phylogenetic analysis of CIPK proteins from 14 plant species revealed that CIPKs in the intron-poor clade originated in seed plants. Tissue-specific expression profiles of CiCBLs and CiCIPKs were analysed, presenting functional diversity. Expression profiles derived from RNA-Seq revealed distinct expression patterns of CiCBLs and CiCIPKs under drought treatment in pecan. Moreover, coexpression network analysis helped to elucidate the relationships between these genes and identify potential candidates for the regulation of drought response, which were verified by qRT–PCR analysis. The characterization and analysis of CBL and CIPK genes in pecan genome could provide a basis for further functional analysis of CiCBLs and CiCIPKs in the drought stress response of pecan. The online version contains supplementary material available at 10.1186/s12870-022-03601-0.
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