Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Plant Non-coding RNAs in the Era of Biological Big Data

Special Issue Editors
Special Issue Information
Keywords
Published Papers

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: closed (30 June 2022) | Viewed by 26526

Share This Special Issue

Special Issue Editors

Prof. Dr. Lin Li

E-Mail Website
Guest Editor

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
Interests: plant systems biology; plant architecture; plant genomics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Mohan B. Singh

E-Mail Website
Guest Editor

Plant Molecular Biology and Biotechnology Laboratory, University of Melbourne, Parkville, Australia
Interests: plant noncoding RNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the advancement of next-generation sequencing, plant biological research has entered the era of big data. It is an exciting time to study plant non-coding RNAs. A large number of non-coding RNAs have been detected to be expressed in a surprisingly wide range of tissue-type or cell-type expression. More and more evidence suggests that non-coding RNAs are involved in a wide range of biological processes. However, many fundamental questions in regard to their mechanism of molecular function remain largely unexplored in plants. In this Special Issue, we call for research papers addressing how different regulatory non-coding RNAs are processed and regulated; how they function in different physiological, developmental, and abiotic and biotic environments; how they interact with proteins and other functional elements to carry out their functions; and finally, how to translate our understanding of non-coding RNAs into plant breeding. 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 non-coding RNAs. Therefore, I warmly welcome original research and review articles in these fields.

Prof. Dr. Lin Li
Prof. Mohan B. Singh
Guest Editors

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
regulatory networks
next-generation sequencing
biological big data
small peptides
plant breeding

Published Papers (10 papers)

Download All Papers

Research

Jump to: Review

20 pages, 3619 KiB

Open AccessArticle

Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

by Tengfei Shen, Yongjie Zheng, Qian Liu, Caihui Chen, Lili Huang, Shaoyong Deng, Meng Xu and Chunxia Yang

Int. J. Mol. Sci. 2022, 23(11), 6321; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116321 - 05 Jun 2022

Cited by 9 | Viewed by 2020

Abstract

Crocins are valuable bioactive components of gardenia fruit, and their biosynthesis and accumulation have attracted widespread interest. Studies have investigated the biosynthesis and accumulation of crocin based on Illumina sequencing, but there is a lack of reports based on full-length transcriptome sequencing. Utilising SMRT sequencing and high-performance liquid chromatography (HPLC), we explored crocin biosynthesis and accumulation in the fruit of Gardenia jasminoides. HPLC analysis showed that crocins specifically exist in fruit and that the content of crocins increases gradually during fruit development. SMRT sequencing generated 46,715 high-quality full-length isoforms, including 5230 novel isoforms that are not present in the G. jasminoides genome. Furthermore, a total of 46 genes and 91 lncRNAs were involved in the biosynthesis and accumulation of crocin. The qRT-PCR indicated that genes involved in crocin biosynthesis reached a peak in the NOV stage. These findings contributed to our understanding of crocin biosynthesis and accumulation. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

17 pages, 3329 KiB

Open AccessArticle

Expression Profiles and Characteristics of Apple lncRNAs in Roots, Phloem, Leaves, Flowers, and Fruit

by Dajiang Wang, Yuan Gao, Simiao Sun, Lianwen Li and Kun Wang

Int. J. Mol. Sci. 2022, 23(11), 5931; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23115931 - 25 May 2022

Cited by 4 | Viewed by 1588

Abstract

LncRNAs impart crucial effects on various biological processes, including biotic stress responses, abiotic stress responses, fertility and development. The apple tree is one of the four major fruit trees in the world. However, lncRNAs’s roles in different tissues of apple are unknown. We identified the lncRNAs in five tissues of apples including the roots, phloem, leaves, flowers, and fruit, and predicted the intricate regulatory networks. A total of 9440 lncRNAs were obtained. LncRNA target prediction revealed 10,628 potential lncRNA–messenger RNA (mRNA) pairs, 9410 pairs functioning in a cis-acting fashion, and 1218 acting in a trans-acting fashion. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to photosynthesis-antenna proteins, single-organism metabolic process and glutathione metabolism. Additionally, a total of 88 lncRNAs have various functions related to microRNAs (miRNAs) as miRNA precursors. Interactions between lncRNAs and miRNAs were predicted, 1341 possible interrelations between 187 mdm-miRNAs and 174 lncRNAs (1.84%) were identified. MSTRG.121644.5, MSTRG.121644.8, MSTRG.2929.2, MSTRG.3953.2, MSTRG.63448.2, MSTRG.9870.2, and MSTRG.9870.3 could participate in the functions in roots as competing endogenous RNAs (ceRNAs). MSTRG.11457.2, MSTRG.138614.2, and MSTRG.60895.2 could adopt special functions in the fruit by working with miRNAs. A further analysis showed that different tissues formed special lncRNA–miRNA–mRNA networks. MSTRG.60895.2–mdm-miR393–MD17G1009000 may participate in the anthocyanin metabolism in the fruit. These findings provide a comprehensive view of potential functions for lncRNAs, corresponding target genes, and related lncRNA–miRNA–mRNA networks, which will increase our knowledge of the underlying development mechanism in apple. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

13 pages, 1655 KiB

Open AccessArticle

Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress

by Qi Tang, Haozhe Lv, Qimeng Li, Xiaoyue Zhang, Le Li, Jie Xu, Fengkai Wu, Qingjun Wang, Xuanjun Feng and Yanli Lu

Int. J. Mol. Sci. 2022, 23(9), 4968; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094968 - 29 Apr 2022

Cited by 7 | Viewed by 2107

Abstract

Maize (Zea mays) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to drought stress in maize roots is unclear. In our study, we found 375 miRNAs in the roots of 16 inbred lines. Of the 16 lines, zma-MIR168, zma-MIR156, and zma-MIR166 were highly expressed, whereas zma-MIR399, zma-MIR2218, and zma-MIR2275 exhibited low expression levels. The expression patterns of miRNA in parental lines and their derived RILs are different. Over 50% of miRNAs exhibited a lower expression in recombinant inbred lines than in parents. The expression of 50 miRNAs was significantly altered under water stress (WS) in at least three inbred lines, and the expression of miRNAs in drought-tolerant lines changed markedly. To better understand the reasons for miRNA response to drought, the degree of histone modifications for miRNA genes was estimated. The methylation level of H3K4 and H3K9 in miRNA precursor regions changed more noticeably after WS, but no such phenomenon was seen for DNA methylation and m6A modification. After the prediction of miRNA targets using psRNATarget and psRobot, we used correlation analysis and qRT-PCR to further investigate the relationship between miRNAs and target genes. We found that 87 miRNA–target pairs were significantly negatively correlated. In addition, a weighted gene co-expression network analysis using miRNAs, as well as their predicted targets, was conducted to reveal that miR159, miR394, and miR319 may be related to maize root growth. The results demonstrated that miRNAs might play essential roles in the response to drought stress. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

19 pages, 4531 KiB

Open AccessArticle

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

by Saeid Babaei, Mohan B. Singh and Prem L. Bhalla

Int. J. Mol. Sci. 2021, 22(19), 10297; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910297 - 24 Sep 2021

Cited by 11 | Viewed by 2304

Abstract

Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

17 pages, 4198 KiB

Open AccessArticle

Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing

by Tengfei Shen, Mengxuan Xu, Haoran Qi, Yuanheng Feng, Zhangqi Yang and Meng Xu

Int. J. Mol. Sci. 2021, 22(18), 10154; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221810154 - 21 Sep 2021

Cited by 14 | Viewed by 2341

Abstract

Xylem is required for the growth and development of higher plants to provide water and mineral elements. The thickening of the xylem secondary cell wall (SCW) not only improves plant survival, but also provides raw materials for industrial production. Numerous studies have found that transcription factors and non-coding RNAs regulate the process of SCW thickening. Pinus massoniana is an important woody tree species in China and is widely used to produce materials for construction, furniture, and packaging. However, the target genes of microRNAs (miRNAs) in the developing xylem of P. massoniana are not known. In this study, a total of 25 conserved miRNAs and 173 novel miRNAs were identified via small RNA sequencing, and 58 differentially expressed miRNAs were identified between the developing xylem (PM_X) and protoplasts isolated from the developing xylem (PM_XP); 26 of these miRNAs were significantly up-regulated in PM_XP compared with PM_X, and 32 were significantly down-regulated. A total of 153 target genes of 20 conserved miRNAs and 712 target genes of 113 novel miRNAs were verified by degradome sequencing. There may be conserved miRNA-mRNA modules (miRNA-MYB, miRNA-ARF, and miRNA-LAC) involved in softwood and hardwood formation. The results of qRT-PCR-based parallel validation were in relatively high agreement. This study explored the potential regulatory network of miRNAs in the developing xylem of P. massoniana and provides new insights into wood formation in coniferous species. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

19 pages, 5311 KiB

Open AccessArticle

ZmFAR1 and ZmABCG26 Regulated by microRNA Are Essential for Lipid Metabolism in Maize Anther

by Yilin Jiang, Ziwen Li, Xinze Liu, Taotao Zhu, Ke Xie, Quancan Hou, Tingwei Yan, Canfang Niu, Shaowei Zhang, Mengbing Yang, Rongrong Xie, Jing Wang, Jinping Li, Xueli An and Xiangyuan Wan

Int. J. Mol. Sci. 2021, 22(15), 7916; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22157916 - 24 Jul 2021

Cited by 26 | Viewed by 2424

Abstract

The function and regulation of lipid metabolic genes are essential for plant male reproduction. However, expression regulation of lipid metabolic genic male sterility (GMS) genes by noncoding RNAs is largely unclear. Here, we systematically predicted the microRNA regulators of 34 maize white brown complex members in ATP-binding cassette transporter G subfamily (WBC/ABCG) genes using transcriptome analysis. Results indicate that the ZmABCG26 transcript was predicted to be targeted by zma-miR164h-5p, and their expression levels were negatively correlated in maize B73 and Oh43 genetic backgrounds based on both transcriptome data and qRT-PCR experiments. CRISPR/Cas9-induced gene mutagenesis was performed on ZmABCG26 and another lipid metabolic gene, ZmFAR1. DNA sequencing, phenotypic, and cytological observations demonstrated that both ZmABCG26 and ZmFAR1 are GMS genes in maize. Notably, ZmABCG26 proteins are localized in the endoplasmic reticulum (ER), chloroplast/plastid, and plasma membrane. Furthermore, ZmFAR1 shows catalytic activities to three CoA substrates in vitro with the activity order of C12:0-CoA > C16:0-CoA > C18:0-CoA, and its four key amino acid sites were critical to its catalytic activities. Lipidomics analysis revealed decreased cutin amounts and increased wax contents in anthers of both zmabcg26 and zmfar1 GMS mutants. A more detailed analysis exhibited differential changes in 54 monomer contents between wild type and mutants, as well as between zmabcg26 and zmfar1. These findings will promote a deeper understanding of miRNA-regulated lipid metabolic genes and the functional diversity of lipid metabolic genes, contributing to lipid biosynthesis in maize anthers. Additionally, cosegregating molecular markers for ZmABCG26 and ZmFAR1 were developed to facilitate the breeding of male sterile lines. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

Review

Jump to: Research

16 pages, 2487 KiB

Open AccessReview

Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects

by Muhammad Haroon, Rabail Afzal, Muhammad Mubashar Zafar, Hongwei Zhang and Lin Li

Int. J. Mol. Sci. 2022, 23(11), 5923; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23115923 - 25 May 2022

Cited by 6 | Viewed by 2189

Abstract

RNA-binding proteins (RBPs) form complex interactions with RNA to regulate the cell’s activities including cell development and disease resistance. RNA-binding proteome (RBPome) aims to profile and characterize the RNAs and proteins that interact with each other to carry out biological functions. Generally, RNA-centric and protein-centric ribonomic approaches have been successfully developed to profile RBPome in different organisms including plants and animals. Further, more and more novel methods that were firstly devised and applied in mammalians have shown great potential to unravel RBPome in plants such as RNA-interactome capture (RIC) and orthogonal organic phase separation (OOPS). Despise the development of various robust and state-of-the-art ribonomics techniques, genome-wide RBP identifications and characterizations in plants are relatively fewer than those in other eukaryotes, indicating that ribonomics techniques have great opportunities in unraveling and characterizing the RNA–protein interactions in plant species. Here, we review all the available approaches for analyzing RBPs in living organisms. Additionally, we summarize the transcriptome-wide approaches to characterize both the coding and non-coding RBPs in plants and the promising use of RBPome for booming agriculture. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

30 pages, 1910 KiB

Open AccessReview

The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response

by Xu Ma, Fei Zhao and Bo Zhou

Int. J. Mol. Sci. 2022, 23(8), 4124; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23084124 - 08 Apr 2022

Cited by 28 | Viewed by 3506

Abstract

Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

20 pages, 1944 KiB

Open AccessReview

Small RNAs Participate in Plant–Virus Interaction and Their Application in Plant Viral Defense

by Zhiqi Deng, Liqun Ma, Peiyu Zhang and Hongliang Zhu

Int. J. Mol. Sci. 2022, 23(2), 696; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23020696 - 08 Jan 2022

Cited by 12 | Viewed by 3434

Abstract

Small RNAs are significant regulators of gene expression, which play multiple roles in plant development, growth, reproductive and stress response. It is generally believed that the regulation of plants’ endogenous genes by small RNAs has evolved from a cellular defense mechanism for RNA viruses and transposons. Most small RNAs have well-established roles in the defense response, such as viral response. During viral infection, plant endogenous small RNAs can direct virus resistance by regulating the gene expression in the host defense pathway, while the small RNAs derived from viruses are the core of the conserved and effective RNAi resistance mechanism. As a counter strategy, viruses evolve suppressors of the RNAi pathway to disrupt host plant silencing against viruses. Currently, several studies have been published elucidating the mechanisms by which small RNAs regulate viral defense in different crops. This paper reviews the distinct pathways of small RNAs biogenesis and the molecular mechanisms of small RNAs mediating antiviral immunity in plants, as well as summarizes the coping strategies used by viruses to override this immune response. Finally, we discuss the current development state of the new applications in virus defense based on small RNA silencing. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures

Figure 1

15 pages, 704 KiB

Open AccessReview

Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants

by Ziwei Li, Peng Tian, Tengbo Huang and Jianzi Huang

Int. J. Mol. Sci. 2021, 22(20), 11205; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222011205 - 18 Oct 2021

Cited by 9 | Viewed by 2712

Abstract

Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices. Full article

(This article belongs to the Special Issue Plant Non-coding RNAs in the Era of Biological Big Data)

► Show Figures