In silico genome-wide analysis of Citrus sinensis (L.) Osbeck NHX and KEA genes and their roles in abiotic stress

IF 1.3 4区生物学 Q3 PLANT SCIENCES Brazilian Journal of Botany Pub Date : 2024-03-05 DOI:10.1007/s40415-024-00981-5

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Abstract

Citrus sinensis (L.) Osbeck is a valuable plant belonging to the Rutaceae family. Stress is induced in plants by abiotic factors such as drought, salinity, and temperature. The monovalent cation proton antiporter (CPA) superfamily, which includes the K⁺ efflux antiporter (KEA) and Na⁺/H⁺ exchanger (NHX) genes, plays a crucial role in the regulation of physiological events. This study aims to identify the KEA and NHX genes of C. sinensis and elucidate the roles of these genes in the response to abiotic stress. For this purpose, phylogenetic structure, distribution of chromosomes, gene duplications, gene and protein structures, cis-acting elements, functional gene ontologies, targeted miRNAs, and in silico PCR primer searches were performed using CsNHX and CsKEA sequences. Two KEA and fifty-five NHX were identified as a result of the analysis. Nine of the fifty-five genes (CsNHX5, CsNHX11, CsNHX12, CsNHX17, CsNHX27, CsNHX28, CsNHX47,CsNHX48, and CsNHX55) have been identified as playing a role in the stress response. On the phylogenetic tree, NHX genes were observed to be divided into three distinct clusters. The existence of multiple segmental and tandem duplications in the CsNHX genes has been demonstrated. Stress-related motifs were identified in the promoter regions of CsKEA and CsNHX by cis-acting element analysis, while stress-related miRNAs were identified by miRNA analysis. Consequently, KEA genes are responsible for transport, but they may also play a role in abiotic stress, as they contain cis-acting elements involved in the stress response and are targeted by miRNAs associated with stress. In addition, it has been determined that CsNHX5, which plays a role in the stress response, has the potential to be used in future transgenic plant production studies as it satisfies the PCR in silico criteria.

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对 Citrus sinensis (L.) Osbeck NHX 和 KEA 基因及其在非生物胁迫中作用的全基因组硅学分析

摘要柑橘（Citrus sinensis (L.) Osbeck）属于芸香科，是一种珍贵的植物。干旱、盐度和温度等非生物因素会对植物产生胁迫。单价阳离子质子拮抗剂（CPA）超家族包括 K+ 外流拮抗剂（KEA）和 Na+/H+ 交换剂（NHX）基因，在生理事件的调控中起着至关重要的作用。本研究旨在鉴定中华鳖的 KEA 和 NHX 基因，并阐明这些基因在非生物胁迫响应中的作用。为此，研究人员利用 CsNHX 和 CsKEA 序列进行了系统发育结构、染色体分布、基因重复、基因和蛋白质结构、顺式作用元件、功能基因本体、目标 miRNAs 和硅 PCR 引物搜索。分析结果确定了两个 KEA 和 55 个 NHX。这 55 个基因中有 9 个（CsNHX5、CsNHX11、CsNHX12、CsNHX17、CsNHX27、CsNHX28、CsNHX47、CsNHX48 和 CsNHX55）被确定在应激反应中发挥作用。在系统发生树上，NHX 基因被观察到分为三个不同的群。CsNHX 基因存在多个节段和串联重复。通过顺式作用元件分析，在 CsKEA 和 CsNHX 的启动子区域发现了与应激有关的图案，而通过 miRNA 分析则发现了与应激有关的 miRNA。因此，KEA 基因负责运输，但也可能在非生物胁迫中发挥作用，因为它们含有参与胁迫反应的顺式作用元件，并被与胁迫相关的 miRNA 靶向。此外，还确定了在应激反应中发挥作用的 CsNHX5 有可能用于未来的转基因植物生产研究，因为它符合 PCR in silico 标准。

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来源期刊

Brazilian Journal of Botany Agricultural and Biological Sciences-Plant Science

CiteScore

3.00

自引率

12.50%

发文量

期刊介绍： The Brazilian Journal of Botany is an international journal devoted to publishing a wide-range of research in plant sciences: biogeography, cytogenetics, ecology, economic botany, physiology and biochemistry, morphology and anatomy, molecular biology and diversity phycology, mycology, palynology, and systematics and phylogeny. The journal considers for publications original articles, short communications, reviews, and letters to the editor. Manuscripts describing new taxa based on morphological data only are suitable for submission; however information from multiple sources, such as ultrastructure, phytochemistry and molecular evidence are desirable. Floristic inventories and checklists should include new and relevant information on other aspects, such as conservation strategies and biogeographic patterns. The journal does not consider for publication submissions dealing exclusively with methods and protocols (including micropropagation) and biological activity of extracts with no detailed chemical analysis.