Identification of differentially-expressed genes potentially implicated in drought response in pitaya (Hylocereus undatus) by suppression subtractive hybridization and cDNA microarray analysis

Fan, Qingjie; Yan, Fangfang; Qiao, Guo; Zhang, Bingxue; Wen, Xiaopeng

doi:10.1016/j.gene.2013.08.098

Cited by 37 publications

(23 citation statements)

References 50 publications

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“…Genes encoding glutathione reductase (GSR) and GGT were identified as important enzymes in glycerophospholipid metabolism. The down-regulation of the GGT gene might play a negative regulatory role in GSH degradation and the GSR gene may have been up-regulated when subjected to drought stress, which consequently mitigated the oxidative stress (Fan et al, 2014 ). In the present study, we observed up-regulation of genes encoding GSR and GGT, suggesting that the two enzymes at least partially contribute to the high drought tolerance in annual ryegrass.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional Profiles of Drought-Related Genes in Modulating Metabolic Processes and Antioxidant Defenses in Lolium multiflorum

et al. 2016

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Drought is a major environmental stress that limits growth and development of cool-season annual grasses. Drought transcriptional profiles of resistant and susceptible lines were studied to understand the molecular mechanisms of drought tolerance in annual ryegrass (Lolium multiflorum L.). A total of 4718 genes exhibited significantly differential expression in two L. multiflorum lines. Additionally, up-regulated genes associated with drought response in the resistant lines were compared with susceptible lines. Gene ontology enrichment and pathway analyses revealed that genes partially encoding drought-responsive proteins as key regulators were significantly involved in carbon metabolism, lipid metabolism, and signal transduction. Comparable gene expression was used to identify the genes that contribute to the high drought tolerance in resistant lines of annual ryegrass. Moreover, we proposed the hypothesis that short-term drought have a beneficial effect on oxidation stress, which may be ascribed to a direct effect on the drought tolerance of annual ryegrass. Evidence suggests that some of the genes encoding antioxidants (HPTs, GGT, AP, 6-PGD, and G6PDH) function as antioxidant in lipid metabolism and signal transduction pathways, which have indispensable and promoting roles in drought resistance. This study provides the first transcriptome data on the induction of drought-related gene expression in annual ryegrass, especially via modulation of metabolic homeostasis, signal transduction, and antioxidant defenses to improve drought tolerance response to short-term drought stress.

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Section: Discussionmentioning

confidence: 99%

Transcriptional Profiles of Drought-Related Genes in Modulating Metabolic Processes and Antioxidant Defenses in Lolium multiflorum

et al. 2016

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“…Hylocereus undatus (H. undatus), is a species of Cactaceae [1]. Based on the commercial value and outstanding nutritional properties, H. undatus is becoming increasingly important to the world [2].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage

Pang

Liu

et al. 2020

Antioxidants

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It has been revealed by us that superoxide scavenging is a new activity of trypsin. In this study, the synergistic mechanisms of trypsin and superoxide dismutases (SODs) were evaluated in Hylocereus undatus (pitaya). Trypsin significantly improved the storage quality of H. undatus, including weight loss impediment and decrease of cellular injury. The regulatory mechanisms of 16 SOD genes by trypsin were revealed using transcriptomic analysis on H. undatus. Results revealed that important physiological metabolisms, such as antioxidant activities or metal ion transport were induced, and defense responses were inhibited by trypsin. Furthermore, the results of protein-protein interaction (PPI) networks showed that besides the entire ROS network, the tiny SODs sub-network was also a scale-free network. Cu/Zn SODs acted as the hub that SODs synergized with trypsin during the storage of H. undatus.Trypsin is a widely used protease. It has been confirmed that trypsin significantly impacts on the free radical scavenging activities of flavonoids [8]. Our previous results also showed that trypsin scavenges superoxide anions (O 2 • − ) and protects cells [9].In the area of phytopathology, transcriptomic analysis has been successful used on lots of plants [10][11][12][13]. However, few of transcriptomic works have been focused on the preservation of fruits. The mechanisms of betalain biosynthesis have been investigated in H. undatus [2], and the concision analysis of antioxidant system induced by trypsin has also been investigated in our previous paper [14]. Considering the superoxide scavenging activity of trypsin, the function and synergistic mechanisms of trypsin with SODs impact on the quality of H. undatus during storage is an interesting work. The mechanisms of postharvest quality of fruits still need more works.Protein-protein interaction (PPI) networks analyses help us to figure out the regulatory mechanisms of proteins [15]. Plugins of Cytoscape, including NetworkAnalyzer, Molecular Complex Detection (MCODE), and cytoHubba, could score and rank the nodes or obtain clusters in the PPI network [16].In the current work, the regulatory mechanisms of trypsin on the H. undatus by cooperating with SODs were investigated. The changes in expression of SODs of H. undatus peels were analyzed. Analyses of gene ontology (GO) and KEGG enrichment of ROS or SOD related genes were performed, and the PPI network of ROS related genes and sub-network of SODs and their first neighbors were constructed. The hub genes of SODs regulated by trypsin during storage were further screened by cytoHubba and MCODE of cytoscape.

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“…The blue color represents a significant difference for dsdw2 versus dsdw, the green color represents a significant difference for dpdw2 versus dpdw, and the grey color represents a significant difference between the two groups (color figure online) (Bhardwaj et al 2013). In addition, nucleotide metabolism was reported to potentially contribute to the drought tolerance of Hylocereus undatus (Fan et al 2014) and Triticum boeoticum (Liu et al 2015). Enriched GO network analysis of dwdp2 (whole plants collected in the rainy season) versus dwdp (whole plants collected in the dry season) (Fig.…”

Section: Discussion 'Response To Stimulus' Conferring Water Deficit Tmentioning

confidence: 99%

Enriched networks ‘nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes’ and ‘response to stimulus’ potentially conferred to drought adaptation of the epiphytic orchid Dendrobium wangliangii

Shi

Senthilkumar

Qiao

et al. 2018

Physiol Mol Biol Plants

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Dendrobium wangliangii is an endangered and epiphytic orchid with tolerance to seasonally extreme arid conditions and occurs exclusively in the hot-dry valley area of southwestern China. To reveal its molecular basis responsible for ecological adaptation, large-scale transcriptome sequencing was performed using Illumina sequencing with pooled mRNA extracted from whole plants and pseudobulbs during drought and rainy seasons. Based on the target transcript selection, the differentially expressed genes were related to 8 well-known droughttolerant categories, and to morphological traits in resistance to water stress including pseudobulbs and roots. Further gene ontology enrichment analysis revealed that 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' were the two most important aspects in resistance to drought stress with respect to the whole plant. In addition, the difference in the number and category of differentially expressed genes in whole plant and stem suggested the involvement of genes specifically localized in the stem, such as GTPbinding protein, lipases, signaling related transcripts and those involved in the ATP metabolic process. The comprehensive analysis of the epiphytic orchid in response to water deprivation indicates that integral tactics lead to active adaptation as a basal defense response to drought stress by the endangered epiphyte, including the collaboration of metabolic processes, responses to a various stimulus and other candidate genes contribute to its extreme drought tolerance. Insights from this study can be further utilized to understand stress-responsive genes in other medicinally important species and to improve the drought tolerance of food crops.

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Identification of differentially-expressed genes potentially implicated in drought response in pitaya (Hylocereus undatus) by suppression subtractive hybridization and cDNA microarray analysis

Cited by 37 publications

References 50 publications

Transcriptional Profiles of Drought-Related Genes in Modulating Metabolic Processes and Antioxidant Defenses in Lolium multiflorum

Transcriptional Profiles of Drought-Related Genes in Modulating Metabolic Processes and Antioxidant Defenses in Lolium multiflorum

Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage

Enriched networks ‘nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes’ and ‘response to stimulus’ potentially conferred to drought adaptation of the epiphytic orchid Dendrobium wangliangii

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