Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
BMC Plant Biol. 2022 Apr 28;22(1):221. doi: 10.1186/s12870-022-03601-0.
Calcium (Ca) serves as a ubiquitous second messenger and plays a pivotal role in signal transduction. Calcineurin B-like proteins (CBLs) are plant-specific Ca sensors that interact with CBL-interacting protein kinases (CIPKs) to transmit Ca 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.
钙（Ca）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（CBLs）是植物特有的 Ca 传感器，与 CBL 相互作用蛋白激酶（CIPKs）相互作用，传递 Ca 信号。已经报道 CBL-CIPK 复合物在植物发育和对干旱胁迫的响应中起着关键作用；然而，关于胡桃基因组中的 CBL 和 CIPK 基因的信息有限，胡桃是一种重要的坚果作物。
在本研究中，从胡桃基因组中总共鉴定出 9 个 CBL 和 30 个 CIPK 基因，并根据系统发育分别分为四个和五个分支。基因结构和保守序列基序分析表明，同一分支中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。片段复制事件对胡桃 CBL 和 CIPK 基因家族的扩张做出了巨大贡献，Ka/Ks 值表明它们都经历了强烈的负选择。来自 14 种植物的 CIPK 蛋白的系统发育分析表明，内含子贫乏分支中的 CIPKs 起源于种子植物。分析 CiCBLs 和 CiCIPKs 的组织特异性表达谱，呈现出功能多样性。来自 RNA-Seq 的表达谱揭示了在干旱处理下胡桃 CiCBLs 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，并鉴定出潜在的候选基因，用于调控干旱响应，这通过 qRT-PCR 分析得到了验证。
胡桃基因组中 CBL 和 CIPK 基因的特征和分析可以为进一步研究 CiCBLs 和 CiCIPKs 在胡桃干旱胁迫响应中的功能提供基础。
