scholarly journals Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11216
Author(s):  
Jianlei Sun ◽  
Yumei Dong ◽  
Chongqi Wang ◽  
Shouhua Xiao ◽  
Zigao Jiao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Regulation Of Gene Expression ◽  
Circular Rnas ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Oxidation Reduction ◽  
Whole Transcriptome Sequencing ◽  
Intergenic Regions ◽  
Whole Transcriptome

Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome’s exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or ‘sponges’ for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.

scholarly journals In Silico Prediction and Functional Characterization of Genes Related to Abiotic and Biotic Stresses in Chickpea (Cicer arietinum)

2018 ◽  
Vol 7 (1) ◽  
pp. 1-35
Author(s):  
Sukhdeep Kaur ◽  
Satendra Singh ◽  
Gitanjali Tandon ◽  
Sarika Jaiswal ◽  
Mir Asif Iquebal ◽  
...  
Keyword(s):  
Cicer Arietinum ◽  
In Silico ◽  
Functional Characterization ◽  
In Silico Prediction ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses

scholarly journals Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247170
Author(s):  
Md. Soyib Hasan ◽  
Vishal Singh ◽  
Shiful Islam ◽  
Md. Sifatul Islam ◽  
Raju Ahsan ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Drought Treatment ◽  
Specific Expression ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Genome Wide

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB) with the lowest binding energy of—5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

scholarly journals The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 461 ◽  
Author(s):  
Ludmila Trilisenko ◽  
Anton Zvonarev ◽  
Airat Valiakhmetov ◽  
Alexey A. Penin ◽  
Irina A. Eliseeva ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phosphate Transport ◽  
Inorganic Polyphosphate ◽  
Oxidative Stresses ◽  
Manganese Uptake ◽  
Oxidation Reduction ◽  
Whole Transcriptome Sequencing ◽  
Essential Function ◽  
Whole Transcriptome

Inorganic polyphosphate (polyP) is crucial for adaptive reactions and stress response in microorganisms. A convenient model to study the role of polyP in yeast is the Saccharomyces cerevisiae strain CRN/PPN1 that overexpresses polyphosphatase Ppn1 with stably decreased polyphosphate level. In this study, we combined the whole-transcriptome sequencing, fluorescence microscopy, and polyP quantification to characterize the CRN/PPN1 response to manganese and oxidative stresses. CRN/PPN1 exhibits enhanced resistance to manganese and peroxide due to its pre-adaptive state observed in normal conditions. The pre-adaptive state is characterized by up-regulated genes involved in response to an external stimulus, plasma membrane organization, and oxidation/reduction. The transcriptome-wide data allowed the identification of particular genes crucial for overcoming the manganese excess. The key gene responsible for manganese resistance is PHO84 encoding a low-affinity manganese transporter: Strong PHO84 down-regulation in CRN/PPN1 increases manganese resistance by reduced manganese uptake. On the contrary, PHM7, the top up-regulated gene in CRN/PPN1, is also strongly up-regulated in the manganese-adapted parent strain. Phm7 is an unannotated protein, but manganese adaptation is significantly impaired in Δphm7, thus suggesting its essential function in manganese or phosphate transport.

scholarly journals Genetic Basis of Follicle Development in Dazu Black Goat by Whole-Transcriptome Sequencing

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3536
Author(s):  
Lu Xu ◽  
Chengli Liu ◽  
Risu Na ◽  
Weiyi Zhang ◽  
Yongmeng He ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Developmental Stages ◽  
Noncoding Rnas ◽  
Circular Rnas ◽  
Follicle Development ◽  
Messenger Rnas ◽  
Molecular Binding ◽  
Whole Transcriptome Sequencing ◽  
Competing Endogenous Rnas ◽  
Whole Transcriptome

The follicle development (FD) is an important factor determining litter size in animals. Recent studies have found that noncoding RNAs (ncRNAs) play an important role in FD. In particular, the role of the regulatory mechanism of competing endogenous RNAs (ceRNAs) that drive FD has attracted increasing attention. Therefore, this study explored the genetic basis of goat FD by obtaining the complete follicular transcriptome of Dazu black goats at different developmental stages. Results revealed that 128 messenger RNAs (mRNAs), 4 long noncoding RNAs (lncRNAs), 49 microRNAs (miRNAs), and 290 circular RNAs (circRNAs) were significantly differentially expressed (DE) between large and small follicles. Moreover, DEmRNAs were enriched in many signaling pathways related to FD, as well as GO terms related to molecular binding and enzyme activity. Based on the analysis of the ceRNA network (CRN), 34 nodes (1 DElncRNAs, 10 DEcircRNAs, 14 DEmiRNAs, and 9 DEmRNAs) and 35 interactions (17 DEcircRNAs–DEmRNAs, 2 DElncRNAs–DEmiRNAs, and 16 DEmRNA–DEmiRNAs) implied that the CRN could be involved in the FD of goats. In conclusion, we described gene regulation by DERNAs and lncRNA/circRNA–miRNA–mRNA CRNs in the FD of goats. This study provided insights into the genetic basis of FD in precise transcriptional regulation.

scholarly journals Genome-wide identification and biochemical characterization of calcineurin B-like calcium sensor proteins in Chlamydomonas reinhardtii

2020 ◽  
Vol 477 (10) ◽  
pp. 1879-1892
Author(s):  
Manoj Kumar ◽  
Komal Sharma ◽  
Akhilesh K. Yadav ◽  
Kajal Kanchan ◽  
Madhu Baghel ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Biochemical Characterization ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Physiological Processes ◽  
Calcineurin B ◽  
Genome Wide ◽  
Dependent Protein ◽  
Sensor Proteins

Calcium (Ca2+) signaling is involved in the regulation of diverse biological functions through association with several proteins that enable them to respond to abiotic and biotic stresses. Though Ca2+-dependent signaling has been implicated in the regulation of several physiological processes in Chlamydomonas reinhardtii, Ca2+ sensor proteins are not characterized completely. C. reinhardtii has diverged from land plants lineage, but shares many common genes with animals, particularly those encoding proteins of the eukaryotic flagellum (or cilium) along with the basal body. Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is an important effector of Ca2+ signaling in animals, while calcineurin B-like proteins (CBLs) play an important role in Ca2+ sensing and signaling in plants. The present study led to the identification of 13 novel CBL-like Ca2+ sensors in C. reinhardtii genome. One of the archetypical genes of the newly identified candidate, CrCBL-like1 was characterized. The ability of CrCBL-like1 protein to sense as well as bind Ca2+ were validated using two-step Ca2+-binding kinetics. The CrCBL-like1 protein localized around the plasma membrane, basal bodies and in flagella, and interacted with voltage-gated Ca2+ channel protein present abundantly in the flagella, indicating its involvement in the regulation of the Ca2+ concentration for flagellar movement. The CrCBL-like1 transcript and protein expression were also found to respond to abiotic stresses, suggesting its involvement in diverse physiological processes. Thus, the present study identifies novel Ca2+ sensors and sheds light on key players involved in Ca2+signaling in C. reinhardtii, which could further be extrapolated to understand the evolution of Ca2+ mediated signaling in other eukaryotes.

scholarly journals Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xing-Zheng Fu ◽  
Xiao-Yong Zhang ◽  
Jie-Ya Qiu ◽  
Xue Zhou ◽  
Meng Yuan ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Copper Toxicity ◽  
Enrichment Analysis ◽  
Circular Rnas ◽  
Potential Threat ◽  
Cu Toxicity ◽  
Citrus Junos ◽  
Whole Transcriptome Sequencing ◽  
Citrus Production ◽  
Whole Transcriptome

Abstract Background Copper (Cu) toxicity has become a potential threat for citrus production, but little is known about related mechanisms. This study aims to uncover the global landscape of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in response to Cu toxicity so as to construct a regulatory network of competing endogenous RNAs (ceRNAs) and to provide valuable knowledge pertinent to Cu response in citrus. Results Tolerance of four commonly used rootstocks to Cu toxicity was evaluated, and ‘Ziyang Xiangcheng’ (Citrus junos) was found to be the most tolerant genotype. Then the roots and leaves sampled from ‘Ziyang Xiangcheng’ with or without Cu treatment were used for whole-transcriptome sequencing. In total, 5734 and 222 mRNAs, 164 and 5 lncRNAs, 45 and 17 circRNAs, and 147 and 130 miRNAs were identified to be differentially expressed (DE) in Cu-treated roots and leaves, respectively, in comparison with the control. Gene ontology enrichment analysis showed that most of the DEmRNAs and targets of DElncRNAs and DEmiRNAs were annotated to the categories of ‘oxidation-reduction’, ‘phosphorylation’, ‘membrane’, and ‘ion binding’. The ceRNA network was then constructed with the predicted pairs of DEmRNAs-DEmiRNAs and DElncRNAs-DEmiRNAs, which further revealed regulatory roles of these DERNAs in Cu toxicity. Conclusions A large number of mRNAs, lncRNAs, circRNAs, and miRNAs in ‘Ziyang Xiangcheng’ were altered in response to Cu toxicity, which may play crucial roles in mitigation of Cu toxicity through the ceRNA regulatory network in this Cu-tolerant rootstock.

scholarly journals Biochemical and histological characterization of tomato mutants

2012 ◽  
Vol 84 (2) ◽  
pp. 573-585 ◽  
Author(s):  
Carolina C. Monteiro ◽  
Milca B. Rolão ◽  
Mônica R. Franco ◽  
Leila P. Peters ◽  
Mariana C. Cia ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Antioxidant Systems ◽  
Guaiacol Peroxidase ◽  
Intercellular Spaces ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Biochemical Responses ◽  
Mda Content ◽  
Anatomical Properties

Biochemical responses inherent to antioxidant systems as well morphological and anatomical properties of photomorphogenic, hormonal and developmental tomato mutants were investigated. Compared to the non-mutant Micro-Tom (MT), we observed that the malondialdehyde (MDA) content was enhanced in the diageotropica (dgt) and lutescent (l) mutants, whilst the highest levels of hydrogen peroxide (H2O2) were observed in high pigment 1 (hp1) and aurea (au) mutants. The analyses of antioxidant enzymes revealed that all mutants exhibited reduced catalase (CAT) activity when compared to MT. Guaiacol peroxidase (GPOX) was enhanced in both sitiens (sit) and notabilis (not) mutants, whereas in not mutant there was an increase in ascorbate peroxidase (APX). Based on PAGE analysis, the activities of glutathione reductase (GR) isoforms III, IV, V and VI were increased in l leaves, while the activity of superoxide dismutase (SOD) isoform III was reduced in leaves of sit, epi, Never ripe (Nr) and green flesh (gf) mutants. Microscopic analyses revealed that hp1 and au showed an increase in leaf intercellular spaces, whereas sit exhibited a decrease. The au and hp1 mutants also exhibited a decreased in the number of leaf trichomes. The characterization of these mutants is essential for their future use in plant development and ecophysiology studies, such as abiotic and biotic stresses on the oxidative metabolism.

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