{"title":"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","authors":"","doi":"10.1007/s40415-024-00981-5","DOIUrl":null,"url":null,"abstract":"<h3>Abstract</h3> <p><em>Citrus sinensis</em> (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 <em>K</em><sup>+</sup> <em>efflux antiporter (KEA)</em> and <em>Na</em><sup>+</sup><em>/H</em><sup>+</sup> <em>exchanger (NHX)</em> genes, plays a crucial role in the regulation of physiological events. This study aims to identify the <em>KEA</em> and <em>NHX</em> genes of <em>C. sinensis</em> 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 <em>CsNHX</em> and <em>CsKEA</em> sequences. Two <em>KEA</em> and fifty-five <em>NHX</em> were identified as a result of the analysis. Nine of the fifty-five genes (<em>CsNHX5, CsNHX11, CsNHX12, CsNHX17, CsNHX27, CsNHX28, CsNHX47,CsNHX48,</em> and <em>CsNHX55</em>) have been identified as playing a role in the stress response. On the phylogenetic tree, <em>NHX</em> genes were observed to be divided into three distinct clusters. The existence of multiple segmental and tandem duplications in the <em>CsNHX</em> genes has been demonstrated. Stress-related motifs were identified in the promoter regions of <em>CsKEA</em> and <em>CsNHX</em> by cis-acting element analysis, while stress-related miRNAs were identified by miRNA analysis. Consequently, <em>KEA</em> 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 <em>CsNHX5</em>, 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.</p>","PeriodicalId":9140,"journal":{"name":"Brazilian Journal of Botany","volume":"10 1","pages":""},"PeriodicalIF":1.4000,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"In silico genome-wide analysis of Citrus sinensis (L.) Osbeck NHX and KEA genes and their roles in abiotic stress\",\"authors\":\"\",\"doi\":\"10.1007/s40415-024-00981-5\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<h3>Abstract</h3> <p><em>Citrus sinensis</em> (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 <em>K</em><sup>+</sup> <em>efflux antiporter (KEA)</em> and <em>Na</em><sup>+</sup><em>/H</em><sup>+</sup> <em>exchanger (NHX)</em> genes, plays a crucial role in the regulation of physiological events. This study aims to identify the <em>KEA</em> and <em>NHX</em> genes of <em>C. sinensis</em> 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 <em>CsNHX</em> and <em>CsKEA</em> sequences. Two <em>KEA</em> and fifty-five <em>NHX</em> were identified as a result of the analysis. Nine of the fifty-five genes (<em>CsNHX5, CsNHX11, CsNHX12, CsNHX17, CsNHX27, CsNHX28, CsNHX47,CsNHX48,</em> and <em>CsNHX55</em>) have been identified as playing a role in the stress response. On the phylogenetic tree, <em>NHX</em> genes were observed to be divided into three distinct clusters. The existence of multiple segmental and tandem duplications in the <em>CsNHX</em> genes has been demonstrated. Stress-related motifs were identified in the promoter regions of <em>CsKEA</em> and <em>CsNHX</em> by cis-acting element analysis, while stress-related miRNAs were identified by miRNA analysis. Consequently, <em>KEA</em> 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 <em>CsNHX5</em>, 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.</p>\",\"PeriodicalId\":9140,\"journal\":{\"name\":\"Brazilian Journal of Botany\",\"volume\":\"10 1\",\"pages\":\"\"},\"PeriodicalIF\":1.4000,\"publicationDate\":\"2024-03-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Brazilian Journal of Botany\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1007/s40415-024-00981-5\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Brazilian Journal of Botany","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s40415-024-00981-5","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
In silico genome-wide analysis of Citrus sinensis (L.) Osbeck NHX and KEA genes and their roles in abiotic stress
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.
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.