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The Role of Non-coding RNA in Plant Response to Stress
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The Role of Non-coding RNA in Plant Response to Stress

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 August 2024 | Viewed by 5458

Special Issue Editor

Dr. Jie Xu

E-Mail Website
Guest Editor
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
Interests: maize noncoding RNA; epitranscriptome; abiotic stress

Special Issue Information

Dear Colleagues,

With the development of molecular biology and sequencing technologies, evidence accumulated over the past decade has begun to unravel that non-coding RNAs (ncRNAs) are widely expressed and have important regulatory functions. Unlike other living forms, plants are sessile, thereby facing severe biotic and abiotic stresses. Recent progress in computational and experimental research has enabled the identification of stress response ncRNAs. However, their mechanism of molecular function remains largely unknown in plants. In this Special Issue, we call for research papers on the characterization and molecular functions of plant abiotic and biotic stress responsive ncRNAs, covering small RNA, long non-coding RNAs, circular RNA, tRNA, and other ncRNAs. We also invite submissions of research articles about the mobility of small RNAs, functional significance of plant ncRNA modifications, and ncRNA structure variations under stress. Here, we would like to provide an integrated platform for the plant research community to share the latest available technologies, methodologies, and new exciting discoveries on plant ncRNAs. Therefore, we warmly welcome original research and review articles in these fields.

Dr. Jie Xu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • non-coding RNAs
  • small RNAs
  • long non-coding RNAs
  • circular RNAs
  • biotic stress
  • abiotic stress
  • RNA modifications
  • RNA structure

Published Papers (5 papers)

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Research

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21 pages, 5992 KiB  
Article
Identification and Analysis of the MIR399 Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress
by Jingjing Liu, Yi Ren, Yan Sun, Yonggang Yin, Bin Han, Lipeng Zhang, Yue Song, Zhen Zhang, Yuanyuan Xu, Dongying Fan, Junpeng Li, Huaifeng Liu and Chao Ma
Int. J. Mol. Sci. 2024, 25(5), 2979; https://doi.org/10.3390/ijms25052979 - 04 Mar 2024
Viewed by 702
Abstract
MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 [...] Read more.
MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 in grapevine, nine members of the Vvi-MIR399 family were identified based on the genome, using a miRBase database search, located on four chromosomes (Chr 2, Chr 10, Chr 15, and Chr 16). The lengths of the Vvi-miR399 precursor sequences ranged from 82 to 122 nt and they formed stable stem–loop structures, indicating that they could produce microRNAs (miRNAs). Furthermore, our results suggested that the 2 to 20 nt region of miR399 mature sequences were relatively conserved among family members. Phylogenetic analysis revealed that the Vvi-MIR399 members of dicots (Arabidopsis, tomato, and sweet orange) and monocots (rice and grapevine) could be divided into three clades, and most of the Vvi-MIR399s were closely related to sweet orange in dicots. Promoter analysis of Vvi-MIR399s showed that the majority of the predicted cis-elements were related to stress response. A total of 66.7% (6/9) of the Vvi-MIR399 promoters harbored drought, GA, and SA response elements, and 44.4% (4/9) of the Vvi-MIRR399 promoters also presented elements involved in ABA and MeJA response. The expression trend of Vvi-MIR399s was consistent in different tissues, with the lowest expression level in mature and young fruits and the highest expression level in stems and young leaves. However, nine Vvi-MIR399s and four target genes showed different expression patterns when exposed to low light, high light, heat, cold, drought, and salt stress. Interestingly, a putative target of Vvi-MIR399 targeted multiple genes; for example, seven Vvi-MIR399s simultaneously targeted VIT_213s0067g03280.1. Furthermore, overexpression of Vvi_MIR399e and Vvi_MIR399f in Arabidopsis enhanced tolerance to drought compared with wild-type (WT). In contrast, the survival rate of Vvi_MIR399d-overexpressed plants were zero after drought stress. In conclusion, Vvi-MIR399e and Vvi-MIR399f, which are related to drought tolerance in grapevine, provide candidate genes for future drought resistance breeding. Full article
(This article belongs to the Special Issue The Role of Non-coding RNA in Plant Response to Stress)
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20 pages, 2692 KiB  
Article
Identification of Tomato microRNAs in Late Response to Trichoderma atroviride
by Rocío Olmo, Narciso M. Quijada, María Eugenia Morán-Diez, Rosa Hermosa and Enrique Monte
Int. J. Mol. Sci. 2024, 25(3), 1617; https://doi.org/10.3390/ijms25031617 - 28 Jan 2024
Viewed by 770
Abstract
The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21–24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, [...] Read more.
The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21–24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant–pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects. Full article
(This article belongs to the Special Issue The Role of Non-coding RNA in Plant Response to Stress)
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23 pages, 6712 KiB  
Article
Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots
by Xin Tang, Qimeng Li, Xiaoju Feng, Bo Yang, Xiu Zhong, Yang Zhou, Qi Wang, Yan Mao, Wubin Xie, Tianhong Liu, Qi Tang, Wei Guo, Fengkai Wu, Xuanjun Feng, Qingjun Wang, Yanli Lu and Jie Xu
Int. J. Mol. Sci. 2023, 24(20), 15039; https://doi.org/10.3390/ijms242015039 - 10 Oct 2023
Viewed by 978
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as [...] Read more.
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m6A), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress. Full article
(This article belongs to the Special Issue The Role of Non-coding RNA in Plant Response to Stress)
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17 pages, 1838 KiB  
Article
Small RNA and Degradome Sequencing in Floral Bud Reveal Roles of miRNAs in Dormancy Release of Chimonanthus praecox
by Ning Liu, Yingjie Jiang, Ting Zhu, Zhineng Li and Shunzhao Sui
Int. J. Mol. Sci. 2023, 24(4), 4210; https://doi.org/10.3390/ijms24044210 - 20 Feb 2023
Cited by 2 | Viewed by 1259
Abstract
Chimonanthus praecox (wintersweet) is highly valued ornamentally and economically. Floral bud dormancy is an important biological characteristic in the life cycle of wintersweet, and a certain period of chilling accumulation is necessary for breaking floral bud dormancy. Understanding the mechanism of floral bud [...] Read more.
Chimonanthus praecox (wintersweet) is highly valued ornamentally and economically. Floral bud dormancy is an important biological characteristic in the life cycle of wintersweet, and a certain period of chilling accumulation is necessary for breaking floral bud dormancy. Understanding the mechanism of floral bud dormancy release is essential for developing measures against the effects of global warming. miRNAs play important roles in low-temperature regulation of flower bud dormancy through mechanisms that are unclear. In this study, small RNA and degradome sequencing were performed for wintersweet floral buds in dormancy and break stages for the first time. Small RNA sequencing identified 862 known and 402 novel miRNAs; 23 differentially expressed miRNAs (10 known and 13 novel) were screened via comparative analysis of breaking and other dormant floral bud samples. Degradome sequencing identified 1707 target genes of 21 differentially expressed miRNAs. The annotations of the predicted target genes showed that these miRNAs were mainly involved in the regulation of phytohormone metabolism and signal transduction, epigenetic modification, transcription factors, amino acid metabolism, and stress response, etc., during the dormancy release of wintersweet floral buds. These data provide an important foundation for further research on the mechanism of floral bud dormancy in wintersweet. Full article
(This article belongs to the Special Issue The Role of Non-coding RNA in Plant Response to Stress)
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Review

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17 pages, 1198 KiB  
Review
MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants
by Ziming Ma and Lanjuan Hu
Int. J. Mol. Sci. 2023, 24(14), 11364; https://doi.org/10.3390/ijms241411364 - 12 Jul 2023
Cited by 5 | Viewed by 1172
Abstract
MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20–24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high [...] Read more.
MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20–24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs’ downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance. Full article
(This article belongs to the Special Issue The Role of Non-coding RNA in Plant Response to Stress)
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