Identification and Expression Analysis of Salinity-induced Genes in Rangpur lime (Citrus limonia)

Şahin‐Çevik, Mehtap; Çevik, Bayram; Çoşkan, Ali

doi:10.1016/j.hpj.2020.07.005

Cited by 7 publications

(9 citation statements)

References 57 publications

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“…Studying transcriptome changes under salt stress in Populus wutunensis which is a salt and drought tolerant species, differentially expressed genes were identified in salt treated leaves that were also involved in ion transport, osmotic regulation, and reactive oxygen species (ROS) scavenging [13]. In another study, gene expression analyses in citrus limonia which is a salt tolerant crop species, revealed upregulation of salinity-induced genes, that were mainly associated with stress response, ion transport, and signalling, regulation of stomatal movement, and oxidative stress [15]. Another transcriptome and gene expression analysis in salt tolerant Suaeda salsa after salt stress treatment, identified DEGs involved in ion transport, reactive oxygen species (ROS) scavenging.…”

Section: Discussionmentioning

confidence: 98%

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Miryeganeh

Saze

2021

IJMS

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Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

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Section: Discussionmentioning

confidence: 98%

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Miryeganeh

Saze

2021

IJMS

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“…It has been proved that Na + accumulation in vacuoles could act as a cheap strategy for osmotic adjustment in plants under high salinity stress ( Glenn and Brown, 1998 ; Wang et al, 2004 ). BASS serves as a Na + /metabolite cotransporter, which could be significantly caused by salt stress ( Huang et al, 2018 ; Şahin-Çevik et al, 2020 ). However, there is only limited information available about the function and regulatory mechanism of salt tolerance in plants.…”

Section: Discussionmentioning

confidence: 99%

Differential Responses to Salt Stress in Four White Clover Genotypes Associated With Root Growth, Endogenous Polyamines Metabolism, and Sodium/Potassium Accumulation and Transport

Geng

Tan

et al. 2022

Front. Plant Sci.

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Selection and utilization of salt-tolerant crops are essential strategies for mitigating salinity damage to crop productivity with increasing soil salinization worldwide. This study was conducted to identify salt-tolerant white clover (Trifolium repens) genotypes among 37 materials based on a comprehensive evaluation of five physiological parameters, namely, chlorophyll (Chl) content, photochemical efficiency of PS II (Fv/Fm), performance index on an absorption basis (PIABS), and leaf relative water content (RWC), and to further analyze the potential mechanism of salt tolerance associated with changes in growth, photosynthetic performance, endogenous polyamine metabolism, and Na+/K+ uptake and transport. The results showed that significant variations in salt tolerance were identified among 37 genotypes, as PI237292 and Tr005 were the top two genotypes with the highest salt tolerance, and PI251432 and Korla were the most salt-sensitive genotypes compared to other materials. The salt-tolerant PI237292 and Tr005 not only maintained significantly lower EL but also showed significantly better photosynthetic performance, higher leaf RWC, underground dry weight, and the root to shoot ratio than the salt-sensitive PI251432 and Korla under salt stress. Increases in endogenous PAs, putrescine (Put), and spermidine (Spd) contents could be key adaptive responses to salt stress in the PI237292 and the Tr005 through upregulating genes encoding Put and Spd biosynthesis (NCA, ADC, SAMDC, and SPDS2). For Na+ and K+ accumulation and transport, higher salt tolerance of the PI237292 could be associated with the maintenance of Na+ and Ca+ homeostasis associated with upregulations of NCLX and BTB/POZ. The K+ homeostasis-related genes (KEA2, HAK25, SKOR, POT2/8/11, TPK3/5, and AKT1/5) are differentially expressed among four genotypes under salt stress. However, the K+ level and K+/Na+ ratio were not completely consistent with the salt tolerance of the four genotypes. The regulatory function of these differentially expressed genes (DEGs) on salt tolerance in the white clover and other leguminous plants needs to be investigated further. The current findings also provide basic genotypes for molecular-based breeding for salt tolerance in white clover species.

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“…The upregulation of these genes under salt stress has recently been reported in a poplar tree ( Populus wutunensis ) as well [ 5 ]. Similarly, transcriptome analysis of a salt tolerant crop species ( Citrus limonia ), and a mangrove tree species ( B. gymnorhiza ) reported upregulation of salinity-responsive genes belonging to the BP categories of salt stress, osmotic stress, ion transport, and ion homeostasis as well [ 7 , 8 ].…”

Section: Discussionmentioning

confidence: 99%

“…Salinity is one of the top and most challenging environmental stressors for plants, and it even leads to other chains of pressures such as osmotic and oxidative stress [ 3 , 4 ]. Many studies in different plant species have reported the changes in expression of salt tolerance genes in response to high salinity (e.g., [ 5 , 6 , 7 , 8 ]). As salt tolerant plants that encounter with constant daily fluctuation of salinity level caused by tidal oscillations, mangroves are a very good model system for studying gene expression changes under natural alteration of salt stress and may help to identify potential salt- and other abiotic-stress response genes [ 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae)

Miryeganeh

Saze

2021

IJMS

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Mangroves are salt-tolerant plant species that grow in coastal saline water and are adapted to harsh environmental conditions. In this study, we de novo assembled and functionally annotated the transcriptome of Rhizophora stylosa, the widely distributed mangrove from the largest mangrove family (Rhizophoraceae). The final transcriptome consists of 200,491 unigenes with an average length, and N50 of 912.7 and 1334 base pair, respectively. We then compared the genome-wide expression profiles between the two morphologically distinct natural populations of this species growing under different levels of salinity depending on their distance from the ocean. Among the 200,491 unigenes, 40,253 were identified as differentially expressed between the two populations, while 15,741 and 24,512 were up- and down-regulated, respectively. Functional annotation assigned thousands of upregulated genes in saline environment to the categories related to abiotic stresses such as response to salt-, osmotic-, and oxidative-stress. Validation of those genes may contribute to a better understanding of adaptation in mangroves species. This study reported, for the first time, the transcriptome of R. stylosa, and the dynamic of it in response to salt stress and provided a valuable resource for elucidation of the molecular mechanism underlying the salt stress response in mangroves and other plants that live under stress.

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Identification and Expression Analysis of Salinity-induced Genes in Rangpur lime (Citrus limonia)

Cited by 7 publications

References 57 publications

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Differential Responses to Salt Stress in Four White Clover Genotypes Associated With Root Growth, Endogenous Polyamines Metabolism, and Sodium/Potassium Accumulation and Transport

The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae)

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