Identification and functional prediction of salt stress-related long noncoding RNAs in grapevine roots

Jin, Zhongxin; Gao, Shiwei; Ma, Wanyun; Lyu, Xinning; Cao, Xiaolei; Yao, Yuxin

doi:10.1016/j.envexpbot.2020.104215

Cited by 17 publications

(15 citation statements)

References 55 publications

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“…Interestingly, the results of target gene enrichment studies of cis regulating genes sequences and eTMs of identified lncRNAs indicated the involvement of serval GO terms towards abiotic stress response like, response to stress, integral component of membrane response to stimulus, regulation of transcription, transcription factor activity and response to chitin (Fig. 5 ) similar to earlier studies in grapes and sorghum (Jin et al 2020 , Sun et al 2020 ).…”

Section: Discussionsupporting

confidence: 84%

“…There are successful examples and reports regarding the involvement of lncRNA in response to abiotic stress in various crop plants like, Gossypium hirsutum for salt stress (Deng et al 2018 ), Brassica juncea for drought (Bhatia et al 2020 ), Medicago truncatula for heat and salt (Wang et al 2015 , Li et al 2019) and Vitis venifera for cold and salinity (Wang et al 2019b , Jin et al 2020 ). Studies in cotton and Medicago under salt stress specifically suggested, lncRNAs are associated actively in plant roots as compared to leaves.…”

Section: Discussionmentioning

confidence: 99%

“…Serval studies have revealed the role of non-coding RNAs in enhancing the salt stress tolerance in plants and modulating the gene expression in grapes, sorghum, wheat etc. (Jin et al 2020, Sun et al 2020, Shumayla et al 2020). These Non-coding RNAs play vital role in gene regulation and are classified into sncRNA (small non coding RNA) and lncRNA (long non-coding RNA) based on their length.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.)

Kumar

Bharadwaj

Sahu

et al. 2021

Physiol Mol Biol Plants

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LncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92–3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.)

Kumar

Bharadwaj

Sahu

et al. 2021

Physiol Mol Biol Plants

View full text Add to dashboard Cite

show abstract

“…Salt stress also altered the accumulation of lncRNAs in Arabidopsis [ 118 ] and Medicago [ 119 ]. Moreover, in grapevine and C. sinensis , 1661 lncRNAs and 172 lncRNAs were found to be differentially expressed in roots under salt stress, respectively [ 120 , 121 ]. Similarly, in cotton, 44 lncRNAs were differentially expressed, of which lncRNA973 was observed to regulate salt stress-responsive genes, including those involved in the ROS scavenging system ( Figure 5 B) [ 122 ].…”

Section: Role Of Lncrnas In Biotic and Abiotic Stressmentioning

confidence: 99%

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Waseem

Liu

Xia

2020

IJMS

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Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.

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“…LncRNAs regulate gene expression through sequence complementarity or homology with RNAs, forming molecular frames for macromolecular complexes [ 29 ]. In plants, lncRNAs function in plant responses to abiotic and biotic stresses and are reportedly involved in modulating salt stress [ 30 ], immunity in A. thaliana against Fusarium oxysporum [ 31 ] and Pseudomonas syringe [ 32 ], plant cold acclimation [ 33 ], as well as plant response to high temperature stress [ 34 ]. A striking regulatory role for lncRNAs in tumour formation has also been extensively documented in animals and humans, including roles in oral squamous cell carcinoma tumorigenesis [ 35 ] and gastric cancer [ 36 ].…”

Section: Introductionmentioning

confidence: 99%

Role of Long Noncoding RNAs ZlMSTRG.11348 and UeMSTRG.02678 in Temperature-Dependent Culm Swelling in Zizania latifolia

Wang

Ning

Luo

et al. 2021

IJMS

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Temperature influences the physiological processes and ecology of both hosts and endophytes; however, it remains unclear how long noncoding RNAs (lncRNAs) modulate the consequences of temperature-dependent changes in host–pathogen interactions. To explore the role of lncRNAs in culm gall formation induced by the smut fungus Ustilago esculenta in Zizania latifolia, we employed RNA sequencing to identify lncRNAs and their potential cis-targets in Z. latifolia and U. esculenta under different temperatures. In Z. latifolia and U. esculenta, we identified 3194 and 173 lncRNAs as well as 126 and four potential target genes for differentially expressed lncRNAs, respectively. Further function and expression analysis revealed that lncRNA ZlMSTRG.11348 regulates amino acid metabolism in Z. latifolia and lncRNA UeMSTRG.02678 regulates amino acid transport in U. esculenta. The plant defence response was also found to be regulated by lncRNAs and suppressed in Z. latifolia infected with U. esculenta grown at 25 °C, which may result from the expression of effector genes in U. esculenta. Moreover, in Z. latifolia infected with U. esculenta, the expression of genes related to phytohormones was altered under different temperatures. Our results demonstrate that lncRNAs are important components of the regulatory networks in plant-microbe-environment interactions, and may play a part in regulating culm swelling in Z. latifolia plants.

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Identification and functional prediction of salt stress-related long noncoding RNAs in grapevine roots

Cited by 17 publications

References 55 publications

Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.)

Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.)

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Role of Long Noncoding RNAs ZlMSTRG.11348 and UeMSTRG.02678 in Temperature-Dependent Culm Swelling in Zizania latifolia

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