Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum

Sun, Xi; Zheng, Hou-Feng; Li, Jinlu; Liu, Luning; Zhang, Xiansheng; Sui, Na

doi:10.3389/fbioe.2020.00331

Cited by 62 publications

(38 citation statements)

References 70 publications

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“…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 ]. Recently, a total of 26 lncRNAs in salt-tolerant M-81E and 133 differentially expressed lncRNAs in salt-sensitive Roma strains of sweet sorghum were identified under salt-stress [ 123 ]. Strand-specific RNA-sequencing of salt-stressed root tissues of two closely related poplars ( Populus euphratica and Populus alba var .…”

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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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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“…Salinity stress is currently an environmental factor that most constraints agricultural productivity (Song and Wang, 2015). Studies have attempted to expand knowledge about functional mechanisms of lncRNAs in response to salt stress as well as in alfalfa (Wang et al, 2015); barley (Karlik and Gozukirmizi, 2018); cotton (Zhang et al, 2019); and sorghum (Sun et al, 2020). In particular, the lncRNA973 overexpression had increased salt tolerance, modulating the expression of cotton salt stress-related genes (Zhang et al, 2019).…”

Section: Lncrna In Crop Plantsmentioning

confidence: 99%

“…Several studies have highlighted the important role of sRNAs in transcriptional and post-transcriptional regulation of gene expression in plants. Although lncRNAs were previously considered to be "transcriptional noise," emerging plant studies have Also, revealed the crucial involvement of lncRNAs in various biological processes including flowering (Fan et al, 2016), development (Zhang and Chen, 2013) and stresses responses (Sun et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress

2021

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Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.

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“…LncRNAs can act as cis-acting or trans-acting factors [34,35], miRNA target mimicry [30], miRNA precursor [36]; and can be involved in histone modi cation [37] as well as DNA methylation [38]. Although the functions and regulation mechanisms of most lncRNAs have not been studied clearly, previous studies indicated that lncRNAs are likely to partake in diversi ed biological processes by regulating the expression of their target genes either in cis-or in trans-acting [30,40,41].…”

Section: Construction Of Expression Pro Le Of 1421 De Lncrnas Provides New Insights Into the Regulation Of Anthocyanin Biosynthesis In Pomentioning

confidence: 99%

A Comparative Transcriptome Analysis of Purple and Yellow Fleshed Potato Tubers Reveals Long Non-coding RNAs and their Targets Functioned in Anthocyanin Biosynthesis

Tang

Dong

et al. 2021

Preprint

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Background: Purple fleshed potato tubers accumulate large amounts of anthocyanin content, servicing as functional foods and high-value feedstock. Long non-coding RNAs (lncRNAs) have been reported to play an important role in anthocyanin synthesis by regulating gene expression in various action modes. However, the mechanism underlying anthocyanin accumulation mediated by lncRNAs in underground organs remains unclear.Results: To excavate the differentially expressed lncRNAs (DE lncRNAs) between purple and yellow fleshed potato tubers, the transcriptome sequencing was performed and a total of 1421 DE lncRNAs were identified. Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that the target genes of these DE lncRNAs were involved in diverse biological processes and pathways for anthocyanin biosynthesis, reflecting the functional diversity of the corresponding lncRNAs. A lncRNA-mRNA interaction network was created based on their correlation to investigate the regulatory relationship among them. Notably, lncRNAs like XLOC_060098 and XLOC_017372 might contribute to anthocyanin synthesis by targeting the key enzyme genes and transcription factor genes in the pathway. Conclusions: The construction of expression profiling of DE lncRNAs and lncRNA-mRNA relationship network is helpful for further unraveling the molecular mechanisms of lncRNAs in anthocyanin synthesis in potato tubers, and provides theory basis for the cultivation of functional potato varieties and the improvement of nutritional quality of other underground crops.

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Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum

Cited by 62 publications

References 70 publications

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

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

From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress

A Comparative Transcriptome Analysis of Purple and Yellow Fleshed Potato Tubers Reveals Long Non-coding RNAs and their Targets Functioned in Anthocyanin Biosynthesis

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