Integrative analysis of long non-coding RNA acting as ceRNAs involved in chilling injury in tomato fruit

Comparative transcriptomics combined with physiological and functional analysis reveals the regulatory mechanism of rainbow trout (Oncorhynchus mykiss) under acute hypoxia stress

Hypoxia, largely triggered by global warming and water contamination, has become an environmental issue of great concern, posing a great threat to aquatic ecosystem. As one of the world's most economically important fish, rainbow trout (Oncorhynchus mykiss) is extremely intolerant of hypoxic environments, however, little is known about the roles of non-coding RNAs (ncRNAs) in the response of rainbow trout to hypoxia stress. Herein, effects of moderate (Tm12L) and severe hypoxia for 12 h (Ts12L) and 12 h reoxygenation on histology, biochemical parameters (antioxidant, metabolism and immunity) and transcriptome (lncRNA, miRNA and mRNA) in rainbow trout liver were investigated. We further validated the regulatory relationships between LOC110519952, novel-m0023-5p and glut1a via dual‑luciferase reporter, overexpression and silencing assays. Compared with Tm12L, the liver in Ts12L showed more severe oxidative damage. Anaerobic, lipid and protein metabolism was enhanced under hypoxia stress, especially in Ts12L. We also found that Tm12L could strengthen innate immune response, which was inhibited in Ts12L. Besides, several hypoxia-related genes (glut1a, vegfaa, hmox, epoa, foxo1a and igfbp1) and ceRNA networks were identified from 1824, 427 and 545 differentially expressed mRNAs, miRNAs and lncRNAs, including LOC118965299-novel-m0179-3p-epoa, LOC110519952-novel-m0023-5p-glut1a, MSTRG.7382.2-miR-184-y-hmox and LOC110520012-miR-206-y-vegfaa. Through in vitro and in vivo functional analysis, we demonstrated that glut1a is a target of novel-m0023-5p, and LOC110519952 can positively regulate glut1a by targeting novel-m0023-5p. Introduction of LOC110519952 could attenuate the promoting effects of novel-m0023-5p on rainbow trout liver cell viability and proliferation. This study highlights the differences in the regulatory mechanism of rainbow trout under different concentrations of hypoxia stress and provides valuable data for further research on the molecular mechanisms of fish adaptation to hypoxic environments.

Emerging roles and mechanisms of lncRNAs in fruit and vegetables

With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.

Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches

Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.

Is winter coming? Impact of the changing climate on plant responses to cold temperature

Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.

Decoding the role of long non-coding RNAs in periodontitis: A comprehensive review

Periodontitis is an inflammatory disease characterized by the pathological loss of alveolar bone and the adjacent periodontal ligament. It is considered a disease that imposes a substantial health burden, with an incidence rate of 20-50%. The etiology of periodontitis is multifactorial, with genetic factors accounting for approximately half of severe cases. Studies have revealed that long non-coding RNAs (lncRNAs) play a pivotal role in periodontitis pathogenesis. Accumulating evidence suggests that lncRNAs have distinct regulatory mechanisms, enabling them to control numerous vital processes in periodontal cells, including osteogenic differentiation, inflammation, proliferation, apoptosis, and autophagy. In this review, we summarize the diverse roles of lncRNAs in the pathogenesis of periodontitis, shedding light on the underlying mechanisms of disease development. By highlighting the potential of lncRNAs as biomarkers and therapeutic targets, this review offers a new perspective on the diagnosis and treatment of periodontitis, paving the way for further investigation into the field of lncRNA-based therapeutics.

Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741

Poplar is an important shelterbelt, timber stand, and city tree species that has been the focus of forestry research. The regulatory role of the long non-coding RNA molecule (lncRNA; length > 200 nt) has been a research hotspot in plants. In this study, seedlings of 741 poplar were irradiated with LED blue and white light, and the Illumina HiSeq 2000 sequencing platform was used to identify lncRNAs. |logFC| > 1 and p < 0.05 were considered to indicate differentially expressed lncRNAs, and nine differentially expressed lncRNAs were screened, the target genes of which were predicted, and three functionally annotated target genes were obtained. The differentially expressed lncRNAs were identified as miRNA targets. Six lncRNAs were determined to be target sites for twelve mRNAs in six miRNA families. LncRNAs and their target genes, including lncRNA MSTRG.20413.1-ptc-miR396e-5p-GRF9, were verified using quantitative real-time polymerase chain reaction analysis, and the expression patterns were analyzed. The analysis showed that the ptc-miR396e-5p expression was downregulated, while lncRNA MSTRG.20413.1 and GRF9 expression was upregulated, after blue light exposure. These results indicate that lncRNAs interact with miRNAs to regulate gene expression and affect plant growth and development.

Research progress of non-coding RNAs in vegetable responses to abiotic stresses

Vegetable crops play a crucial role in agricultural production, providing essential vitamins and minerals necessary for a healthy diet. Recently, there has been growing interest in cultivating vegetable varieties with outstanding agricultural and economic traits. However, vegetable production is often exposed to various abiotic stresses like soil drought, temperature fluctuations, and heavy metal stress, which can negatively impact yield and quality. While previous research has investigated the physiological responses of vegetable crops to such stressors, less attention has been given to genetic networks. Plants respond to environmental stress mainly by adapting first and then reacting, thereby enhancing their resistance to stress. Typically, different abiotic stresses trigger epigenetic changes, which can regulate non-coding RNAs. Therefore, studying the epigenetic mechanisms of vegetable crop responses to abiotic stress can provide insights into the molecular response mechanisms of plants under stress. This knowledge has practical applications in breeding vegetable crops for resistance. This article summarizes the primary research findings on the regulation of non-coding RNAs and their expression levels in vegetable crops exposed to abiotic stresses to guide molecular breeding approaches for vegetable crops.

Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs

Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.

Functional Relevance of the Long Intergenic Non-Coding RNA Regulator of Reprogramming (Linc-ROR) in Cancer Proliferation, Metastasis, and Drug Resistance

Cancer is responsible for more than 10 million deaths every year. Metastasis and drug resistance lead to a poor survival rate and are a major therapeutic challenge. Substantial evidence demonstrates that an increasing number of long non-coding RNAs are dysregulated in cancer, including the long intergenic non-coding RNA, regulator of reprogramming (linc-ROR), which mostly exerts its role as an onco-lncRNA acting as a competing endogenous RNA that sequesters micro RNAs. Although the properties of linc-ROR in relation to some cancers have been reviewed in the past, active research appends evidence constantly to a better comprehension of the role of linc-ROR in different stages of cancer. Moreover, the molecular details and some recent papers have been omitted or partially reported, thus the importance of this review aimed to contribute to the up-to-date understanding of linc-ROR and its implication in cancer tumorigenesis, progression, metastasis, and chemoresistance. As the involvement of linc-ROR in cancer is elucidated, an improvement in diagnostic and prognostic tools could promote and advance in targeted and specific therapies in precision oncology.

Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit

Non-coding RNAs play vital roles in the diverse biological processes of plants, and they are becoming key topics in horticulture research. In particular, miRNAs and long non-coding RNAs (lncRNAs) are receiving increased attention in fruit crops. Recent studies in horticulture research provide both genetic and molecular evidence that miRNAs and lncRNAs regulate biological function and stress responses during fruit development. Here, we summarize multiple regulatory modules of miRNAs and lncRNAs and their biological roles in fruit sets and stress responses, which would guide the development of molecular breeding techniques on horticultural crops.

miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses

Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.

Role of long non coding RNA in plants under abiotic and biotic stresses

Evolutionary processes have evolved plants to cope with several different natural stresses. Basic physiological activities of crop plants are significantly harmed by these stresses, reducing productivity and eventually leading to death. The recent advancements in high-throughput sequencing of transcriptome and expression profiling with NGS techniques lead to the innovation of various RNAs which do not code for proteins, more specifically long non-coding RNAs (lncRNAs), undergirding regulate growth, development, and the plant defence mechanism transcriptionally under stress situations. LncRNAs are a diverse set of RNAs that play key roles in various biological processes at the level of transcription, post-transcription, and epigenetics. These are thought to serve crucial functions in plant immunity and response to changes in the environment. In plants, however, just a few lncRNAs have been functionally identified. In this review, we will address recent advancements in comprehending lncRNA regulatory functions, focusing on the expanding involvement of lncRNAs in modulating environmental stress responsiveness in plants.

Emerging role of lncRNAs in drug resistance mechanisms in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) originates in the squamous cell lining the mucosal surfaces of the head and neck region, including the oral cavity, nasopharynx, tonsils, oropharynx, larynx, and hypopharynx. The heterogeneity, anatomical, and functional characteristics of the patient make the HNSCC a complex and difficult-to-treat disease, leading to a poor survival rate and a decreased quality of life due to the loss of important physiologic functions and aggressive surgical injury. Alteration of driver-oncogenic and tumor-suppressing lncRNAs has recently been recently in HNSCC to obtain possible biomarkers for diagnostic, prognostic, and therapeutic approaches. This review provides current knowledge about the implication of lncRNAs in drug resistance mechanisms in HNSCC. Chemotherapy resistance is a major therapeutic challenge in HNSCC in which lncRNAs are implicated. Lately, it has been shown that lncRNAs involved in autophagy induced by chemotherapy and epithelial–mesenchymal transition (EMT) can act as mechanisms of resistance to anticancer drugs. Conversely, lncRNAs involved in mesenchymal–epithelial transition (MET) are related to chemosensitivity and inhibition of invasiveness of drug-resistant cells. In this regard, long non-coding RNAs (lncRNAs) play a pivotal role in both processes and are important for cancer detection, progression, diagnosis, therapy response, and prognostic values. As the involvement of more lncRNAs is elucidated in chemoresistance mechanisms, an improvement in diagnostic and prognostic tools could promote an advance in targeted and specific therapies in precision oncology.

Identification and analysis of miRNAs-lncRNAs-mRNAs modules involved in stem-elongation of deepwater rice (Oryza sativa L.)

Deepwater is an abiotic stress that limits rice cultivation worldwide due to recurrent floods. The miRNAs and lncRNAs are two non-coding RNAs emerging as major regulators of gene expressions under different abiotic stresses. However, the regulation of these two non-coding RNAs under deepwater stress in rice is still unexplored. In this study, small RNA-seq and RNA-seq from internode and node tissues were analyzed to predict deepwater stress responsive miRNAs and lncRNAs, respectively. Additionally, a competitive endogenous RNA (ceRNA) study revealed about 69 and 25 lncRNAs acting as endogenous target mimics (eTM) with the internode and node miRNAs, respectively. In ceRNA analyses, some of the key miRNAs such as miR1850.1, miR1848, and IN-nov-miR145 were upregulated while miR159e was downregulated, and their respective eTM lncRNAs and targets were found to have opposite expressions. Moreover, we have transiently expressed one module (IN-nov-miR145-Cc-TCONS_00011544-Os11g36430.3) in tobacco leaves. The integrated analysis has identified differentially expressed (DE) miRNAs, lncRNAs and their target genes, and the complex regulatory network, which might lead to stem elongation under deepwater stress. In this novel attempt to identify and characterize miRNAs and lncRNAs under deepwater stress in rice, we have provided, probably for the first time, a reference platform to study the interactions of these two non-coding RNAs with respective target genes through transient expression analyses.

Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening

LncRNAs represent a class of RNA transcripts of more than 200 nucleotides (nt) in length without discernible protein-coding potential. The expression levels of lncRNAs are significantly affected by stress or developmental cues. Recent studies have shown that lncRNAs participate in fruit development and ripening processes in tomato and strawberry; however, in other fleshy fruits, the association between lncRNAs and fruit ripening remains largely elusive. Here, we constructed 9 ssRNA-Seq libraries from three different peach (Prunus persica) fruit developmental stages comprising the first and second exponential stages and the fruit-ripening stage. In total, 1500 confident lncRNAs from 887 loci were obtained according to the bioinformatics analysis. The lncRNAs identified in peach fruits showed distinct characteristics compared with protein-coding mRNAs, including lower expression levels, lower complexity of alternative splicing, shorter isoforms and smaller numbers of exons. Expression analysis identified 575 differentially expressed lncRNAs (DELs) classified into 6 clusters, among which members of Clusters 1, 2, 4 and 5 were putatively associated with fruit development and ripening processes. Quantitative real-time PCR revealed that the DELs indeed had stage-specific expression patterns in peach fruits. GO and KEGG enrichment analysis revealed that DELs might be associated with fruit-ripening-related physiological and metabolic changes, such as flavonoid biosynthesis, fruit texture softening, chlorophyll breakdown and aroma compound accumulation. Finally, the similarity analysis of lncRNAs within different plant species indicated the low sequence conservation of lncRNAs. Our study reports a large number of fruit-expressed lncRNAs and identifies fruit development phase-specific expressed lncRNA members, which highlights their potential functions in fruit development and ripening processes and lays the foundations for future functional research.

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

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.

Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

Background

Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown.

Results

The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes.

Conclusion

The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08470-3.

Overexpression of lncRNA08489 enhances tomato immunity against Phytophthora infestans by decoying miR482e-3p

LncRNAs are widely involved in various biological processes of plants. Recent evidences indicated that lncRNAs could act as competing endogenous RNAs (ceRNAs) to adsorb complementary miRNAs in a type of target mimicry, thereby indirectly regulating the target genes of miRNAs. In this study, a lncRNA, lncRNA08489 was identified to be the ceRNA of miR482e-3p in tomato plants. The expression patterns of lncRNA08489 and miR482e-3p showed opposite trends after tomato plants infected with Phytophthora infestans. In tomato leaves overexpressing lncRNA08489 (OE08489), the expression level of miR482e-3p decreased and its target gene, NBS-LRR increased. After infection with P. infestans, the resistance of OE08489 plants was stronger than that of the wild type, and the reactive oxygen species (ROS) scavenging ability of OE08489 plants was significantly improved. Taken together, these results indicated that lncRNA08489 acted as a ceRNA to decoy miR482e-3p and regulate the expression of NBS-LRR to enhance tomato resistance through ROS-scavenging system.

Revealing the Specific Regulations of Brassinolide on Tomato Fruit Chilling Injury by Integrated Multi-Omics

Tomato fruit is susceptible to chilling injury (CI) when stored at low temperatures, limiting its storage potential, and resulting in economic loss if inappropriate temperatures are used. Brassinolide (BR) is a plant growth regulator that is known to decrease the susceptibility of fruit to CI. In this study, transcriptome, metabolome, and proteome analysis revealed the regulation mechanism of BR treatment in alleviating tomato fruit CI. The results showed that the differentially expressed metabolites mainly included amino acids, organic acids, carbohydrates, and lipids. Differentially expressed genes (DEGs) were involved in plant cold stress response (HSFA3, SHSP, and TPR), fruit redox process (POD, PAL, and LOX), related to the fruit texture (CESA, β-Gal, and PAE), plant hormone signal transduction (ACS3, ARF, and ERF,), transcription factors (TCP, bHLH, GATA). Moreover, differentially expressed proteins were associated with fruit texture (CESA, PE, PL, and CHI), plant oxidation processes (LOX, GPX, CAT, and POD), plant cold stress response (HSF, HSP20, HSP70, and HSP90B), plant hormone signal transduction (BSK1 and JAR1) and transcription factors (WRKY and MYB). Our study showed that BR alleviates CI symptoms of tomato fruit by regulating LOX in the α-linolenic acid metabolism pathway, enhancing jasmonic acid-CoA (JA-CoA) synthesis, inhibiting cell wall and membrane lipid damage. The results provided a theoretical basis for further study on the CI mechanism of tomato fruit.

Analysis of long non-coding RNAs and mRNAs in harvested kiwifruit in response to the yeast antagonist, Wickerhamomyces anomalus

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W. anomalus exhibits good biocontrol activity against blue and gray mold on kiwifruit.

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LncRNAs in kiwifruit may be involved in activating plant hormone signal transduction pathways in response to the biocontrol yeast.

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LncRNAs in kiwifruit may modulate the production of related TFs and secondary metabolites.

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The expression of downstream defense-related genes in kiwifruit increases in response to the application of the biocontrol yeast.

Biological control utilizing antagonistic yeasts is an effective method for controlling postharvest diseases. Long non-coding RNAs (lncRNAs) have been found to be involved in a variety of plant growth and development processes, including those associated with plant disease resistance. In the present study, the yeast antagonist, Wickerhamomyces anomalus, was found to strongly inhibit postharvest blue mold (Penicillium expansum) and gray mold (Botrytis cinerea) decay of kiwifruit. Additionally, lncRNA high-throughput sequencing and bioinformatic analysis was used to identify lncRNAs in W. anomalus-treated wounds in kiwifruit and predict their function based on putative target genes. Our results indicate that lncRNAs may be involved in increasing ethylene (ET), jasmonic acid (JA), abscisic acid (ABA), and auxin (IAA) levels, as well as activating signal transduction pathways that regulate the expression of several transcription factors (WRKY72, WRKY53, JUB1AP2). These transcription factors (TFs) then mediate the expression of downstream, defense-related genes (ZAR1, PAD4, CCR4, NPR4) and the synthesis of secondary metabolites, thus, potentially enhancing disease resistance. Notably, by stimulating the accumulation of antifungal compounds, such as phenols and lignin, disease resistance in kiwifruit was enhanced. Our study provides new information on the mechanism underlying the induction of disease resistance in kiwifruit by W. anomalus, as well as a new disease resistance strategy that can be used to enhance the defense response of fruit to pathogenic fungi.

Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing

As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.

Comparative transcriptome combined with transgenic analysis reveal the involvement of salicylic acid pathway in the response of Nicotiana tabacum to triclosan stress

Triclosan (TCS) is a highly effective antibacterial agent, which is widely distributed in wastewater and sludge. The application of sludge containing high concentration TCS in agriculture will cause physiological damage to plants. Nevertheless, little is known about the physiological and molecular mechanism of TCS to plants. So firstly the physiological and biochemical indexes of tobacco with treatment of different concentrations of TCS were evaluated in this study. The results showed that tobacco plants with TCS treatment exhibited lower germination rate, root development, photosynthesis efficiency, and higher ROS accumulation in comparison with control group. The transcriptome analysis of tobacco plants was then performed to reveal the molecular mechanism in the response of tobacco to TCS. There were 3, 819 differentially expressed genes (DEGs) were identified between groups with or without TCS treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these DEGs were mainly enriched in groups of the plant hormone signal transduction pathway. To further investigate the role of plant hormone, transgenic tobacco overexpressing a homologous of salicylic acid (SA) binding protein gene was used to assess the SA-mediate TCS tolerance in plant. The results showed that transgenic plants exhibited enhanced activities of antioxidant enzymes and stronger TCS resistance than wild-type ones, which verify the important role of SA signal pathway in TCS response of tobacco plants. This study could be used to better understand the key roles of plant hormones in the TCS stress response of higher plants, and find key pathways and candidate genes for phytoremediation.

Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Simple Summary

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. However, the roles of long non-coding RNAs (lncRNAs) in the interaction between plants and viruses is unclear, particularly for the Chinese wheat mosaic virus (CWMV) interaction. In this study, we used a deep RNA sequencing strategy to profile lncRNAs involved in the response to CWMV infection in Nicotiana benthamiana and analyzed differentially expressed lncRNAs that responded to CWMV infection, using a bioinformatics method. We identified 1175 new lncRNAs in N. benthamiana infected with CWMV, with 65 lncRNAs showing differential expression. These lncRNAs were mainly enriched in plant hormone signal transduction and other pathways according to GO and KEGG pathway enrichment analyses. In addition, differential expression of XLOC_006393 after CWMV infection may be the precursor of NbmiR168c, which can respond to CWMV infection by modulating the expression of its target gene NbAGO1. We believe that our study makes a significant contribution to the literature because these results provide a valuable resource for studying lncRNAs involved in CWMV infection and improving the understanding of the molecular mechanism of CWMV infection.

Abstract

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening

Kiwifruit has gained increasing attention worldwide for its unique flavor and high nutritional value. Rapid softening after harvest greatly shortens its shelf-life and reduces the commercial value. Therefore, it is imperative and urgent to identify and clarify its softening mechanism. This study aimed to analyze and compare the long noncoding RNA (lncRNA) and mRNA expression patterns in ABA-treated (ABA) and room temperature (RT)-stored fruits with those in freshly harvested fruits (CK) as control. A total of 697 differentially expressed genes (DEGs) and 81 differentially expressed lncRNAs (DELs) were identified while comparing ABA with CK, and 458 DEGs and 143 DELs were detected while comparing RT with CK. The Kyoto Encyclopedia of Genes and Genomes analysis of the identified DEGs and the target genes of DELs revealed that genes involved in starch and sucrose metabolism, brassinosteroid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis accounted for a large part. The co-localization networks, including 38 DEGs and 31 DELs in ABA vs. CK, and 25 DEGs and 25 DELs in RT vs. CK, were also performed. Genes related to fruit ripening, such as genes encoding β-galactosidase, mannan endo-1,4-β-mannosidase, pectinesterase/pectinesterase inhibitor, and NAC transcription factor, were present in the co-localization network, suggesting that lncRNAs were involved in regulating kiwifruit ripening. Notably, several ethylene biosynthesis- and signaling-related genes, including one 1-aminocyclopropane-1-carboxylic acid oxidase gene and three ethylene response factor genes, were found in the co-localization network of ABA vs. CK, suggesting that the promoting effect of ABA on ethylene biosynthesis and fruit softening might be embodied by increasing the expression of these lncRNAs. These results may help understand the regulatory mechanism of lncRNAs in ripening and ABA-induced fruit softening of kiwifruit.

Interactions and links among the noncoding RNAs in plants under stresses

The complex interplay among sRNAs, lncRNAs and circRNAs has been implicated in plants under biotic and abiotic stresses. Here, we review current advances in our understanding of ncRNA interactions and links, which have considerable potential for improving the agronomic traits and the environmental adaptability of plants. Plants can respond to biotic or abiotic stresses. To cope with various conditions, numerous intricate molecular regulatory mechanisms have evolved in plants. Noncoding RNAs (ncRNAs) can be divided into small noncoding RNAs (sRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). Emerging evidence has demonstrated that interplay among the ncRNAs acts as a novel layer in the regulatory mechanisms, which has attracted substantial interest. Links between sRNAs can affect plant immune responses and development in synergistic or antagonistic manners. Additionally, multiple interactions between lncRNAs and sRNAs are involved in crop breeding, disease resistance and high tolerance to environmental stresses. Here, we summarize current knowledge of the interactions and links among the ncRNAs in plant responses to stresses and the methods for identifying ncRNA interactions. Furthermore, challenges and prospects for further progress in elucidating ncRNA interactions and links are highlighted.

Genome-wide lncRNAs identification and association analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L.)

Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. The spectacular progress made in next-generation sequencing technologies has enabled a genome-wide identification of lncRNAs in multiple plant species. In this study, a genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparing a tolerant variety, Kongyu131 (KY131) and a sensitive variety, Dongnong422 (DN422). A total of 1485 lncRNAs were identified, and 566 of these lncRNAs were defined as differential lncRNAs by comparing four samples. GO and KEGG enrichment analyses were performed, focusing on the cis- and trans- target genes of the differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate 35 cold-tolerant QTLs at the booting stage. In summary, 12 candidate genes and their target lncRNAs were identified by qRT-PCR. LncTar was used to identify the interaction between lncRNAs and the candidate genes. In addition, 130 rice cultivars with rich genetic diversity were collected to verify the association of candidate genes with cold-resistance. The results revealed that five SNPs in LOC_Os07g42940, three SNP and one InDel in LOC_Os02g03410 were associated with cold-resistance at a significant level using association analysis. This study provides new gene resources and insights into cold-resistance research for rice.

Noncoding RNAs: functional regulatory factors in tomato fruit ripening

Tomato has emerged as the model system for investigations into the regulation of fleshy-fruit ripening and senescence, and the ripening process involving the coordinated regulation at the gene/chromatin/epigenetic, transcriptional, post-transcriptional and protein levels. Noncoding RNAs play important roles in fruit ripening as important transcriptional and post-transcriptional regulatory factors. In this review, we systematically summarize the recent advances in the regulation of tomato fruit ripening involved in ethylene biosynthesis and signal transduction, fruit pigment accumulation, fruit flavor and aroma, fruit texture by noncoding RNAs and their coordinate regulatory network model were set up and also suggest future directions for the functional regulations of noncoding RNAs on tomato fruit ripening.

LncRNA improves cold resistance of winter wheat by interacting with miR398

One of the important functions of long non-coding RNA (lncRNA) is to be competing endogenous RNAs (ceRNAs). As miR398 is reported to respond to different stressors, it is necessary to explore its relationship with lncRNA in the cold resistance mechanism of winter wheat. Tae-miR398-precursor sequence was isolated from the winter wheat (Triticum aestivum). RLM-RACE verified that tae-miR398 cleaved its target CSD1. Quantitative detection at 5°C, -10°C and -25°C showed that the expression of tae-miR398 decreased in response to low temperatures, whereas CSD1 showed an opposite expression pattern. LncR9A, lncR117 and lncR616 were predicted and verified to interact with miR398. tae-miR398 and three lncRNAs were transferred into Arabidopsis thaliana respectively. The lncR9A were transferred into Brachypodium distachyom. Transgenic plants were cultivated at -8°C and assessed for the expression of malondialdehyde, chlorophyll, superoxide dismutase and miR398-lncRNA-target mRNA. The results demonstrate that tae-miR398 regulates low temperature tolerance by downregulating its target, CSD1. lncRNA regulates the expression of CSD1 indirectly by competitively binding miR398, which, in turn, affects the resistance of Dn1 to cold. miR398-regulation triggers a regulatory loop that is critical to cold stress tolerance in wheat. Our findings offer an improved strategy to crop plants with enhanced stress tolerance.

Identification of tomato circular RNAs responsive to Phytophthora infestans

Circular RNAs (circRNAs), a novel branch of noncoding RNAs, are widespread in eukaryotic cells. Particularly, due to their abilities to bind microRNA (miRNA) and serve as "sponges", circRNAs can regulate gene expression and participate in multiple biological processes. To detect the function of the circRNAs in tomato resistance, in our study, high-throughput sequencing were used to detect the circRNAs in tomatoes before and after Phytophthora infestans (P. infestans) infection. A total of 68 circRNAs were identified, of them, 18 (26%) were termed as exonic circRNAs, 33 (49%) were termed as intergenic circRNAs, 17 (25%) were termed as intronic circRNAs. Thirty-six out of 68 circRNAs differentially expressed in tomatoes after infection, including 9 up- and 27 down-regulated. Among the up-regulated circRNAs, two exoinc circRNAs, circRNA45 and circRNA47 were annotated as whitefly-induced gp91-phox and ethylene-forming enzyme, respectively. Both of them could act as miR477-3p sponge. Transgenic plants transiently overexpressed circRNA45 and circRNA47 both displayed smaller lesion area than the control plants upon infection, accompanied by lower expression levels of miR477-3p. Furthermore, transiently overexpression of miR477-3p in tomatoes leading to a decline in their targeted disease related genes expression. Our results firstly identified circRNAs in tomato upon P. infestans infection and demonstrated that circRNA45 and circRNA47 may act as positive regulators in tomato resistance by regulating miRNA-mRNAs expression levels.

Engineering Multiple Abiotic Stress Tolerance in Canola, Brassica napus

Impacts of climate change like global warming, drought, flooding, and other extreme events are posing severe challenges to global crop production. Contribution of Brassica napus towards the oilseed industry makes it an essential component of international trade and agroeconomics. Consequences from increasing occurrences of multiple abiotic stresses on this crop are leading to agroeconomic losses making it vital to endow B. napus crop with an ability to survive and maintain yield when faced with simultaneous exposure to multiple abiotic stresses. For an improved understanding of the stress sensing machinery, there is a need for analyzing regulatory pathways of multiple stress-responsive genes and other regulatory elements such as non-coding RNAs. However, our understanding of these pathways and their interactions in B. napus is far from complete. This review outlines the current knowledge of stress-responsive genes and their role in imparting multiple stress tolerance in B. napus. Analysis of network cross-talk through omics data mining is now making it possible to unravel the underlying complexity required for stress sensing and signaling in plants. Novel biotechnological approaches such as transgene-free genome editing and utilization of nanoparticles as gene delivery tools are also discussed. These can contribute to providing solutions for developing climate change resilient B. napus varieties with reduced regulatory limitations. The potential ability of synthetic biology to engineer and modify networks through fine-tuning of stress regulatory elements for plant responses to stress adaption is also highlighted.

Identification of lncRNAs and their regulatory relationships with target genes and corresponding miRNAs in melon response to powdery mildew fungi

Melon (Cucumis melo L.), an economically beneficial crop widely cultivated around the world, is vulnerable to powdery mildew (PM). However, the studies on molecular mechanism of melon response to PM fungi is still limited. Long non coding RNAs (lncRNAs) have emerged as new regulators in plants response to biotic stresses. We predicted and identified the intricate regulatory roles of lncRNAs in melon response to PM fungi. A total of 539 lncRNAs were identified from PM-resistant (MR-1) and susceptible melon (Top Mark), in which 254 were significantly altered after PM fungi infection. Multiple target genes of lncRNAs were found to be involved in the hydrolysis of chitin, callose deposition and cell wall thickening, plant-pathogen interaction and plant hormone signal transduction pathway. Additionally, a total of 42 lncRNAs possess the various functions with microRNAs (miRNAs), including lncRNAs that are targeted by miRNAs and function as miRNA precursors or miRNA sponges. These findings provide a comprehensive view of potentially functional lncRNAs, corresponding target genes and related lncRNA-miRNA pairs, which will greatly increase our knowledge of the mechanism underlying susceptibility and resistance to PM in melon.

Overexpression of the Long Noncoding RNA FOXD2-AS1 Promotes Cisplatin Resistance in Esophageal Squamous Cell Carcinoma Through the miR-195/Akt/mTOR Axis

Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) mediate the development of esophageal squamous cell carcinoma (ESCC) via various pathophysiological pathways. This study explored the impact of the lncRNA FOXD2-AS1 on cisplatin resistance in ESCC and its possible mechanisms. Upregulation of FOXD2-AS was detected in patients with ESCC and ESCC cells that are resistant to cisplatin. In an in vitro assay, knockdown of FOXD2-AS1 noticeably inhibited cell invasion and growth, triggered cell death, and repressed the stimulation of the Akt/mTOR axis in cisplatin-resistant ESCC cells (TE-1/DDP). Conversely, the overexpression of FOXD2-AS1 remarkably increased cell invasion and growth, repressed cell death, and triggered the stimulation of the Akt/mTOR axis in TE-1/DDP cells. These findings, along with bioinformatics and validation tests, showed that FOXD2-AS1 targeted miR-195 by acting as a competing endogenous RNA. FOXD2-AS1/miR-195/Akt/mTOR axis plays a crucial role in resistance to cisplatin in ESCC cells, offering an innovative strategy to treat ESCC.

Integrative comparative analyses of metabolite and transcript profiles uncovers complex regulatory network in tomato (Solanum lycopersicum L.) fruit undergoing chilling injury

Tomato fruit are especially susceptible to chilling injury (CI) when continuously exposed to temperatures below 12 °C. In this study, integrative comparative analyses of transcriptomics and metabolomics data were performed to uncover the regulatory network in CI tomato fruit. Metabolite profiling analysis found that 7 amino acids, 27 organic acids, 16 of sugars and 22 other compounds had a significantly different content while transcriptomics data showed 1735 differentially expressed genes (DEGs) were down-regulated and 1369 were up-regulated in cold-stored fruit. We found that the contents of citrate, cis-aconitate and succinate were increased, which were consistent with the expression of ATP-citrate synthase (ACS) and isocitrate dehydrogenase (IDH) genes in cold-treated tomato fruit. Cold stress promotes the expression of ACS and IDH which may increase the synthesis of citrate, cis-aconitate and succinate. Alanine and leucine had increased contents, which may result from alanine aminotransferase (ALT) and branched-chain amino acid aminotransferase (BcAT)'s high expression levels, respectively. Overall the transcriptomics and metabolomics data in our study explain the molecular mechanisms of the chilling injury and expands our understanding of the complex regulatory mechanisms of a metabolic network in response to chilling injury in tomato fruit.

Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction

Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS-Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.