Genome-wide identification of long non-coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber green mottle mosaic virus infection in watermelon

lncRNAs and epigenetics regulate plant's resilience against biotic stresses

With the advent of transcriptomic techniques involving single-stranded RNA sequencing and chromatin isolation by RNA purification-based sequencing, transcriptomic studies of coding and non-coding RNAs have been executed efficiently. These studies acknowledged the role of non-coding RNAs in modulating gene expression. Long non-coding RNAs (lncRNAs) are a kind of non-coding RNAs having lengths of >200 nucleotides, playing numerous roles in plant developmental processes such as photomorphogenesis, epigenetic changes, reproductive tissue development, and in regulating biotic and abiotic stresses. Epigenetic changes further control gene expression by changing their state to "ON-OFF" and also regulate stress memory and its transgenerational inheritance. With well-established regulatory mechanisms, they act as guides, scaffolds, signals, and decoys to modulate gene expression. They act as a major operator of post-transcriptional modifications such as histone and epigenetic modifications, and DNA methylations. The review elaborates on the roles of lncRNAs in plant immunity and also discusses how epigenetic markers alter gene expression in response to pest/pathogen attack and influences chromatin-associated stress memory as well as transgenerational inheritance of epigenetic imprints in plants. The review further summarizes some research studies on how histone modifications and DNA methylations resist pathogenic and pest attacks by activating defense-related genes.

CircRNA: An emerging star in plant research: A review

CircRNAs are a class of covalently closed non-coding RNA formed by linking the 5' terminus and the 3' terminus after reverse splicing. CircRNAs are widely found in eukaryotes, and they are highly conserved, with spatio-temporal expression specificity and stability. CircRNAs can act as miRNA sponges to regulate the expression of downstream target genes, regulating the transcription of parental genes and some can even be translated into peptides or proteins. Research on circRNAs in plants is still in its infancy compared to that in animals. With the deepening of research, the results of a variety of plant circRNAs suggest that they play an important role in growth and development, and tolerance towards abiotic stresses such as salt, drought, low temperature, high temperature and other adverse environments. In this review paper, we elaborated the molecular characteristics, mechanism of action, function and bioinformatics databases of plant circRNAs, combined with the progress of circRNA research in animals, discussed the potential mechanism of action of plant circRNAs, and proposed the unsolved problems and prospects for future application of plant circRNAs.

Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress

Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.

Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions

Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.

miRNAs for crop improvement

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.

Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction

In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.

Integrated agronomic, physiological, microstructure, and whole-transcriptome analyses reveal the role of biomass accumulation and quality formation during Se biofortification in alfalfa

Se-biofortified agricultural products receive considerable interest due to the worldwide severity of selenium (Se) deficiency. Alfalfa (Medicago sativa L.), the king of forage, has a large biomass, a high protein content, and a high level of adaptability, making it a good resource for Se biofortification. Analyses of agronomic, quality, physiological, and microstructure results indicated the mechanism of biomass increase and quality development in alfalfa during Se treatment. Se treatment effectively increased Se content, biomass accumulation, and protein levels in alfalfa. The enhancement of antioxidant capacity contributes to the maintenance of low levels of reactive oxygen species (ROS), which, in turn, serves to increase alfalfa's stress resistance and the stability of its intracellular environment. An increase in the rate of photosynthesis contributes to the accumulation of biomass in alfalfa. To conduct a more comprehensive investigation of the regulatory networks induced by Se treatment, the transcriptome sequencing of non-coding RNA (ncRNA) was employed to compare 100 mg/kg Se treatment and control groups. The analysis identified 1,414, 62, and 5 genes as DE-long non-coding RNAs (DE-lncRNA), DE-microRNAs (DE-miRNA), and DE-circular RNA (DE-circRNA), respectively. The function of miRNA-related regulatory networks during Se biofortification in alfalfa was investigated. Subsequent enrichment analysis revealed significant involvement of transcription factors, DNA replication and repair mechanisms, photosynthesis, carbohydrate metabolism, and protein processing. The antioxidant capacity and protein accumulation of alfalfa were regulated by the modulation of signal transduction, the glyoxalase pathway, proteostasis, and circRNA/lncRNA-related regulatory networks. The findings offer new perspectives on the regulatory mechanisms of Se in plant growth, biomass accumulation, and stress responses, and propose potential strategies for enhancing its utilization in the agricultural sector.

Genome-wide identification and characterization of tissue-specific non-coding RNAs in black pepper (Piper nigrum L.)

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are the two classes of non-coding RNAs (ncRNAs) present predominantly in plant cells and have various gene regulatory functions at pre- and post-transcriptional levels. Previously deemed as "junk", these ncRNAs have now been reported to be an important player in gene expression regulation, especially in stress conditions in many plant species. Black pepper, scientifically known as Piper nigrum L., despite being one of the most economically important spice crops, lacks studies related to these ncRNAs. From a panel of 53 RNA-Seq datasets of black pepper from six tissues, namely, flower, fruit, leaf, panicle, root, and stem of six black pepper cultivars, covering eight BioProjects across four countries, we identified and characterized a total of 6406 lncRNAs. Further downstream analysis inferred that these lncRNAs regulated 781 black pepper genes/gene products via miRNA-lncRNA-mRNA network interactions, thus working as competitive endogenous RNAs (ceRNAs). The interactions may be various mechanisms like miRNA-mediated gene silencing or lncRNAs acting as endogenous target mimics (eTMs) of the miRNAs. A total of 35 lncRNAs were also identified to be potential precursors of 94 miRNAs after being acted upon by endonucleases like Drosha and Dicer. Tissue-wise transcriptome analysis revealed 4621 circRNAs. Further, miRNA-circRNA-mRNA network analysis showed 432 circRNAs combining with 619 miRNAs and competing for the binding sites on 744 mRNAs in different black pepper tissues. These findings can help researchers to get a better insight to the yield regulation and responses to stress in black pepper in endeavor of higher production and improved breeding programs in black pepper varieties.

Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon

Male sterility is a valuable trait for watermelon breeding, as watermelon hybrids exhibit obvious heterosis. However, the underlying regulatory mechanism is still largely unknown, especially regarding the related non-coding genes. In the present study, approximately 1035 differentially expressed genes (DEGs), as well as 80 DE-lncRNAs and 10 DE-miRNAs, were identified, with the overwhelming majority down-regulated in male-sterile floral buds. Enrichment analyses revealed that the general phenylpropanoid pathway as well as its related metabolisms was predicted to be altered in a mutant compared to its fertile progenitor. Meanwhile, the conserved genetic pathway DYT1-TDF1-AMS-MS188-MS1, as well as the causal gene ClAMT1 for the male-sterile mutant Se18, was substantially disrupted during male reproductive development. In addition, some targets of the key regulators AMS and MS188 in tapetum development were also down-regulated at a transcriptional level, such as ABCG26 (Cla004479), ACOS5 (Cla022956), CYP703A2 (Cla021151), PKSA (Cla021099), and TKPR1 (Cla002563). Considering lncRNAs may act as functional endogenous target mimics of miRNAs, competitive endogenous RNA networks were subsequently constructed, with the most complex one containing three DE-miRNAs, two DE-lncRNAs, and 21 DEGs. Collectively, these findings not only contribute to a better understanding of genetic regulatory networks underlying male sterility in watermelon, but also provide valuable candidates for future research.

Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.

From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.

LncRNA-mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato

Sweet potato (Ipomoea batatas L.) is considered a highly nutritional and economical crop due to its high contents of bioactive substances, such as anthocyanin and chlorogenic acid (CGA), especially in leaves and stems. The roles of noncoding RNAs (ncRNA), including long noncoding RNA (lncRNA) and microRNA (miRNA), in CGA synthesis, are still unknown. In this study, the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs in two leafy vegetable genotypes "FS7-6-14-7" (high CGA content) and "FS7-6" (low CGA content) were identified. The cis-regulation between lncRNA and mRNA was analyzed. Then, the CGA synthesis-related modules MEBlue and MEYellow were identified to detect trans-regulation mRNA-lncRNA pairs. The GO and KEGG annotations suggested that mRNA in these two modules was significantly enriched in the secondary metabolite synthesis biosynthesis category. A competing endogenous RNAs (ceRNA) network, including 8730 miRNA-mRNA and 444 miRNA-lncRNA pairs, was constructed by DEmiRNA target prediction. Then, a CGA synthesis-related ceRNA network was obtained with lncRNA and mRNA from MEBlue and MEYellow. Finally, one relational pair, MSTRG.47662.1/mes-miR398/itb04g00990, was selected for functional validation. Overexpression of lncRNA MSTRG.47662.1 and mRNA itb04g00990 increased CGA content in both tobacco and sweet potato callus, while overexpression of miRNA mes-miR398 decreased CGA content. Meanwhile, regression analysis of the expression patterns demonstrated that MSTRG.47662.1, acting as a ceRNA, promoted itb04g00990 expression by competitively binding mes-miR398 in CGA synthesis in sweet potato. Our results provide insights into how ncRNA-mediated ceRNA regulatory networks likely contribute to CGA synthesis in leafy sweet potato.

Regulatory non-coding RNA: The core defense mechanism against plant pathogens

Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.

New insights on circular RNAs and their potential applications as biomarkers, therapeutic agents, and preventive vaccines in viral infections: with a glance at SARS-CoV-2

The occurrence of viral infections and approaches to handling them are very challenging and require prompt diagnosis and timely treatment. Recently, genomic medicine approaches have come up with the discovery of the competing endogenous RNA (ceRNA) network, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) on the basis of gene silencing. CircRNAs, as a group of non-encoded RNAs, make a loop-like structure by back-splicing through 3′ and 5′ ends. They are stable, abundant, specific, and highly conserved and can be quickly generated at large scales in vitro. CircRNAs have the potential to contribute in several cellular processes in a way that some serve as microRNA sponges, cellular transporters, protein-binding RNAs, transcriptional regulators, and immune system modulators. CircRNAs can even play an important role in modulating antiviral immune responses. In the present review, circRNAs’ biogenesis, function, and biomarker and therapeutic potential as well as their prospective applications as vaccines against viral infections such as SARS-CoV-2 are explained. By considering their unique properties, their potential to be used as novel vaccines, biomarkers, and a therapeutic approach appears possible.

B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2-3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10-15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.

Long Non-Coding RNAs as Emerging Regulators of Pathogen Response in Plants

Long non-coding RNAs (lncRNAs) are transcripts without protein-coding potential that contain more than 200 nucleotides that play important roles in plant survival in response to different stresses. They interact with molecules such as DNA, RNA, and protein, and play roles in the regulation of chromatin remodeling, RNA metabolism, and protein modification activities. These lncRNAs regulate the expression of their downstream targets through epigenetic changes, at the level of transcription and post-transcription. Emerging information from computational biology and functional characterization of some of them has revealed their diverse mechanisms of action and possible roles in biological processes such as flowering time, reproductive organ development, as well as biotic and abiotic stress responses. In this review, we have mainly focused on the role of lncRNAs in biotic stress response due to the limited availability of knowledge in this domain. We have discussed the available molecular mechanisms of certain known lncRNAs against specific pathogens. Further, considering that fungal, viral, and bacterial diseases are major factors in the global food crisis, we have highlighted the importance of lncRNAs against pathogen responses and the progress in plant research to develop a better understanding of their functions and molecular mechanisms.

LncRNA-mediated ceRNA networks provide novel potential biomarkers for peanut drought tolerance

Drought stress has been the major constraint on peanut yield and quality, and an understanding of the function of long non-coding (lncRNAs) in the peanut drought stress response is still in its infancy. In this study, two peanut varieties with contrasting drought tolerance were used to explore the functions of lncRNAs in the peanut drought response, and the results showed that the drought-tolerant variety presented greater antioxidant enzyme activity, osmotic adjustment ability, and photosynthesis under drought conditions. There were 4329 lncRNAs identified in the two varieties, of which 535 and 663 lncRNAs were differentially expressed in NH5 and FH18, respectively. The cis targets of the differentially expressed lncRNAs were putatively involved in secondary metabolite biosynthesis and other basic metabolic processes. A total of 673 competing endogenous RNA (ceRNA) pairs were selected specifically in NH5, and the associated ceRNA network revealed six lncRNAs, MSTRG.70535.2, MSTRG.86570.2, MSTRG.86570.1, MSTRG.100618.1, MSTRG.81214.2, and MSTRG.30931.1were considered as hub nodes. They were speculated to contribute to enhancing peanut drought tolerance, such as regulating transcription and plant growth processes, thereby improving the drought stress response. In this study, lncRNAs and mRNAs interaction networks were constructed to aid a comprehensive understanding of the peanut drought stress response and form a basis for future research.

Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes

Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.

Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics

Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus-plant interactions, as well as the characterization of viral RNA modifications.

NGS Methodologies and Computational Algorithms for the Prediction and Analysis of Plant Circular RNAs

Circular RNAs (circRNAs) are a class of single-stranded RNAs derived from exonic, intronic, and intergenic regions from precursor messenger RNAs (pre-mRNA), where a noncanonical back-splicing event occurs, in which the 5' and 3' ends are attached by covalent bond. CircRNAs participate in the regulation of gene expression at the transcriptional and posttranscriptional level primarily as miRNA and RNA-binding protein (RBP) sponges, but also involved in the regulation of alternative RNA splicing and transcription. CircRNAs are widespread and abundant in plants where they have been involved in stress responses and development. Through the analysis of all publications in this field in the last five years, we can summarize that the identification of these molecules is carried out through next generation sequencing studies, where samples have been previously treated to eliminate DNA, rRNA, and linear RNAs as a means to enrich circRNAs. Once libraries are prepared, they are sequenced and subsequently studied from a bioinformatics point of view. Among the different tools for identifying circRNAs, we can highlight CIRI as the most used (in 60% of the published studies), as well as CIRCExplorer (20%) and find_circ (20%). Although it is recommended to use more than one program in combination, and preferably developed specifically to treat with plant samples, this is not always the case. It should also be noted that after identifying these circular RNAs, most of the authors validate their findings in the laboratory in order to obtain bona fide results.

Host-virus interactions mediated by long non-coding RNAs

Viruses are obligate pathogens that cause a wide range of diseases across all kingdoms of life. They have a colossal impact on the economy and healthcare infrastructure world-wide. Plants and animals have developed sophisticated molecular mechanisms to defend themselves against viruses and viruses in turn hijack host mechanisms to ensure their survival inside their hosts. Long non-coding (lnc) RNAs have emerged as important macromolecules that regulate plant-virus and animal-virus interactions. Both pro-viral and anti-viral lncRNAs have been reported and they show immense potential to be used as markers and in therapeutics. The current review is focussed on the recent developments that have been made in viral interactions of animals and plants.

Systematic Identification and Functional Analysis of Circular RNAs During Rice Black-Streaked Dwarf Virus Infection in the Laodelphax striatellus (Fallén) Midgut

Circular RNAs (circRNAs) are endogenous RNAs that have critical regulatory roles in numerous biological processes. However, it remains largely unknown whether circRNAs are induced in response to plant virus infection in the insect vector of the virus as well as whether the circRNAs regulate virus infection. Rice black-streaked dwarf virus (RBSDV) is transmitted by Laodelphax striatellus (Fallén) in a persistent propagative manner and causes severe losses in East Asian countries. To explore the expression and function of circRNAs in the regulation of virus infection, we determined the circRNA expression profile in RBSDV-free or RBSDV-infected L. striatellus midgut tissues by RNA-Seq. A total of 2,523 circRNAs were identified, of which thirteen circRNAs were differentially expressed after RBSDV infection. The functions of these differentially circRNAs were predicted by GO and KEGG pathway analyses. The expression changes of five differentially expressed circRNAs and eight parental genes were validated by RT-qPCR. The circRNAs-microRNAs (miRNAs) interaction networks were analyzed and two miRNAs, which were predicted to bind circRNAs, were differentially expressed after virus infection. CircRNA2030 was up-regulated after RBSDV infection in L. striatellus midgut. Knockdown of circRNA2030 by RNA interference inhibited the expression of its predicted parental gene phospholipid-transporting ATPase (PTA) and enhanced RBSDV infection in L. striatellus. However, none of the six miRNAs predicting to bind circRNA2030 was up-regulated after circRNA2030 knockdown. The results suggested that circRNA2030 might affect RBSDV infection via regulating PTA. Our results reveal the expression profile of circRNAs in L. striatellus midgut and provide new insight into the roles of circRNAs in virus-insect vector interaction.

Long Noncoding RNAs in Plant Viroids and Viruses: A Review

Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs.

Sl-lncRNA15492 interacts with Sl-miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans

Long non-coding RNAs (lncRNAs) are involved in the resistance of plants to infection by pathogens via interactions with microRNAs (miRNAs). Long non-coding RNAs are cleaved by miRNAs to produce phased small interfering RNAs (phasiRNAs), which, as competing endogenous RNAs (ceRNAs), function as decoys for mature miRNAs, thus inhibiting their expression, and contain pre-miRNA sequences to produce mature miRNAs. However, whether lncRNAs and miRNAs mediate other molecular mechanisms during plant resistance to pathogens is unknown. In this study, as a positive regulator, Sl-lncRNA15492 from tomato (Solanum lycopersicum Zaofen No. 2) plants affected tomato resistance to Phytophthora infestans. Gain- and loss-of-function experiments and RNA ligase-mediated 5'-amplification of cDNA ends (RLM-5' RACE) also revealed that Sl-miR482a was negatively involved in tomato resistance by targeting Sl-NBS-LRR genes and that silencing of Sl-NBS-LRR1 decreased tomato resistance. Sl-lncRNA15492 inhibited the expression of mature Sl-miR482a, whose precursor was located within the antisense sequence of Sl-lncRNA15492. Further degradome analysis and additional RLM-5' RACE experiments verified that mature Sl-miR482a could also cleave Sl-lncRNA15492. These results provide a mechanism by which lncRNAs might inhibit precursor miRNA expression through antisense strands of lncRNAs, and demonstrate that Sl-lncRNA15492 and Sl-miR482a mutually inhibit the maintenance of Sl-NBS-LRR1 homeostasis during tomato resistance to P. infestans.