Zia Komal, Rao Muhammad Junaid, Sadaqat Muhammad, Azeem Farrukh, Fatima Kinza, Tahir Ul Qamar Muhammad, Alshammari Abdulrahman, Alharbi Metab
Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China.
Front Genet. 2022 Oct 11;13:1034921. doi: 10.3389/fgene.2022.1034921. eCollection 2022.
Cyclic nucleotide-gated channels (CNGC) gene family has been found to be involved in physiological processes including signaling pathways, environmental stresses, plant growth, and development. This gene family of non-selective cation channels is known to regulate the uptake of calcium and is reported in several plant species. The pangenome-wide studies enable researchers to understand the genetic diversity comprehensively; as a comparative analysis of multiple plant species or member of a species at once helps to better understand the evolutionary relationships and diversity present among them. In the current study, pangenome-wide analysis of the CNGC gene family has been performed on five Citrus species As a result, a total of 32 genes in , 27 genes in , 30 genes in , 31 genes in and 30 genes in were identified. In addition, two unique genes and were identified, which may have potential roles. All the identified CNGC genes were unevenly distributed on 9 chromosomes except had genes distributed on 7 chromosomes and were classified into four major groups and two sub-groups namely I, II, III, IV-A, and IV-B. Cyclic nucleotide binding (CNB) motif, calmodulin-binding motif (CaMB), and motif for IQ-domain were conserved in Citrus Intron exon structures of citrus species were not exactly as same as the gene structures of . The majority of cis-regulatory elements (CREs) were light responsive and others include growth, development, and stress-related indicating potential roles of the CNGC gene family in these functions. Both segmental and tandem duplication were involved in the expansion of the CNGC gene family in Citrus The miRNAs are involved in the response of CsCNGC genes towards drought stress along with having regulatory association in the expression of these genes. Protein- Protein interaction (PPI) analysis also showed the interaction of CNGC proteins with other CNGCs which suggested their potential role in pathways regulating different biological processes. GO enrichment revealed that CNGC genes were involved in the transport of ions across membranes. Furthermore, tissue-specific expression patterns of leaves sample of were studied under drought stress. Out of 32 genes of 3 genes i.e., , and were highly up-regulated, and only was highly down-regulated. The qRT-PCR analysis also showed that CNGC genes were highly expressed after treatment with drought stress, while gene expression was lower under controlled conditions. This work includes findings based on multiple genomes instead of one, therefore, this will provide more genomic information rather than single genome-based studies. These findings will serve as a basis for further functional insights into the CNGC gene family.
环核苷酸门控通道（CNGC）基因家族已被发现参与包括信号通路、环境胁迫、植物生长和发育等生理过程。这个非选择性阳离子通道基因家族已知可调节钙的吸收，并且在几种植物物种中都有报道。泛基因组范围的研究使研究人员能够全面了解遗传多样性；因为同时对多个植物物种或一个物种的成员进行比较分析有助于更好地理解它们之间的进化关系和多样性。在当前的研究中，对五个柑橘物种进行了CNGC基因家族的泛基因组范围分析。结果，在[具体物种1]中鉴定出总共32个基因，在[具体物种2]中鉴定出27个基因，在[具体物种3]中鉴定出30个基因，在[具体物种4]中鉴定出31个基因，在[具体物种5]中鉴定出30个基因。此外，还鉴定出两个独特的基因[基因名称1]和[基因名称2]，它们可能具有潜在作用。所有鉴定出的CNGC基因除了[具体物种6]有基因分布在7条染色体上外，在9条染色体上分布不均，并被分为四个主要组和两个亚组，即I、II、III、IV - A和IV - B。环核苷酸结合（CNB）基序、钙调蛋白结合基序（CaMB）和IQ结构域基序在柑橘中是保守的。柑橘物种的内含子外显子结构与[对比物种]的基因结构并不完全相同。大多数顺式调控元件（CREs）是光响应性的，其他的包括与生长、发育和胁迫相关的，这表明CNGC基因家族在这些功能中具有潜在作用。片段重复和串联重复都参与了柑橘中CNGC基因家族的扩增。miRNA参与了CsCNGC基因对干旱胁迫的响应，同时在这些基因的表达中具有调控关联。蛋白质 - 蛋白质相互作用（PPI）分析还显示CNGC蛋白与其他CNGC之间的相互作用，这表明它们在调节不同生物过程的途径中具有潜在作用。基因本体（GO）富集分析表明CNGC基因参与跨膜离子运输。此外，研究了[具体物种]叶片样本在干旱胁迫下的组织特异性表达模式。在[具体物种]的32个基因中，有3个基因，即[基因名称3]、[基因名称4]和[基因名称5]高度上调，只有[基因名称6]高度下调。qRT - PCR分析还表明，干旱胁迫处理后CNGC基因高度表达，而在对照条件下基因表达较低。这项工作基于多个基因组而非单个基因组的研究结果，因此，这将提供比基于单个基因组的研究更多的基因组信息。这些发现将为进一步深入了解CNGC基因家族的功能提供基础。
