Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress

Genome-wide analysis of long noncoding RNAs in response to salt stress in Nicotiana tabacum

BACKGROUND

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the response of plants to various abiotic stresses, including drought, heat and salt stress. However, the identification and characterization of genome-wide salt-responsive lncRNAs in tobacco (Nicotiana tabacum L.) have been limited. Therefore, this study aimed to identify tobacco lncRNAs in roots and leaves in response to different durations of salt stress treatment.

RESULTS

A total of 5,831 lncRNAs were discovered, with 2,428 classified as differentially expressed lncRNAs (DElncRNAs) in response to salt stress. Among these, only 214 DElncRNAs were shared between the 2,147 DElncRNAs in roots and the 495 DElncRNAs in leaves. KEGG pathway enrichment analysis revealed that these DElncRNAs were primarily associated with pathways involved in starch and sucrose metabolism in roots and cysteine and methionine metabolism pathway in leaves. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 15 co-expression modules, with four modules strongly linked to salt stress across different treatment durations (MEsalmon, MElightgreen, MEgreenyellow and MEdarkred). Additionally, an lncRNA-miRNA-mRNA network was constructed, incorporating several known salt-associated miRNAs such as miR156, miR169 and miR396.

CONCLUSIONS

This study enhances our understanding of the role of lncRNAs in the response of tobacco to salt stress. It provides valuable information on co-expression networks of lncRNA and mRNAs, as well as networks of lncRNAs-miRNAs-mRNAs. These findings identify important candidate lncRNAs that warrant further investigation in the study of plant-environment interactions.

Roles of long non-coding RNAs in plant immunity

Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.

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.

Long Non-Coding RNAs: New Players in Plants

During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.

Comparative transcriptome profiling of Polianthes tuberosa during a compatible interaction with root-knot nematode Meloidogyne incognita

BACKGROUND

The root-knot nematode (RKN; Meloidogyne spp.) is the most destructive plant parasitic nematode known to date. RKN infections, especially those caused by Meloidogyne incognita, are one of the most serious diseases of tuberose.

METHODS AND RESULTS

To investigate the molecular mechanism in the host-pathogen interactions, the Illumina sequencing platform was employed to generate comparative transcriptome profiles of uninfected and Meloidogyne incognita-infected tuberose plants, during early, mid, and late infection stage. A total of 7.5 GB (49 million reads) and 9.3 GB (61 million reads) of high-quality data was generated for the control and infected samples, respectively. These reads were combined and assembled using the Trinity assembly program which clustered them into 1,25,060 unigenes. A total of 85,360 validated CDS were obtained from the combined transcriptome whereas 6,795 CDS and 7,778 CDS were found in the data for the control and infected samples, respectively. Gene ontology terms were assigned to 958 and 1,310 CDSs from the control and infected data, respectively. The KAAS pathway analysis revealed that 1,248 CDS in the control sample and 1,482 CDS in the infected sample were enriched with KEGG pathways. The major proportions of CDS were annotated for carbohydrate metabolism, signal transduction and translation related pathways in control and infected samples. Of the 8,289 CDS commonly expressed between the control and infected plants, 256 were significantly upregulated and 129 were significantly downregulated in the infected plants.

CONCLUSIONS

Collectively, our results provide a comprehensive gene expression changes in tuberose during its association with RKNs and point to candidate genes that are involved in nematode stress signaling for further investigation. This is the first report addressing genes associated with M. incognita-tuberose interaction and the results have important implications for further characterization of RKN resistance genes in tuberose.

Pattern-triggered immunity against root-knot nematode infection: A minireview

Pattern-triggered immunity (PTI) is the basal level of defense a plant has against pathogens. In the case of root-knot nematodes (RKN), PTI relies on the recognition of nematode-associated molecular patterns (NAMPs) for activation. Nematodes have successfully overcome PTI many times by evolving effector proteins to combat PTI responses. As a result, much study has focused on effector-triggered immunity (ETI). Here, we highlight recent advances in our understanding of PTI against RKN. A new interest in understanding PTI in response to RKN infection shows that understanding the basal defense responses RKN have overcome provides critical insight into what mechanisms the effectors have evolved to target in the host plant.

Regulatory long non-coding RNAs in root growth and development

As sessile organisms, plants have evolved sophisticated mechanisms of gene regulation to cope with changing environments. Among them, long non-coding RNAs (lncRNAs) are a class of RNAs regulating gene expression at both transcriptional and post-transcriptional levels. They are highly responsive to environmental cues or developmental processes and are generally involved in fine-tuning plant responses to these signals. Roots, in addition to anchoring the plant to the soil, allow it to absorb the major part of its mineral nutrients and water. Furthermore, roots directly sense environmental constraints such as mineral nutrient availability and abiotic or biotic stresses and dynamically adapt their growth and architecture. Here, we review the role of lncRNAs in the control of root growth and development. In particular, we highlight their action in fine-tuning primary root growth and the development of root lateral organs, such as lateral roots and symbiotic nodules. Lastly, we report their involvement in plant response to stresses and the regulation of nutrient assimilation and homeostasis, two processes leading to the modification of root architecture. LncRNAs could become interesting targets in plant breeding programs to subtly acclimate crops to coming environmental changes.

Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L

Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.

Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage

Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01059-2.

Genetic toolbox and regulatory circuits of plant-nematode associations

Plant-nematode associations are the most imperative area of study that forms the basis to understand their regulatory networks and coordinated functional aspects. Nematodes are highly parasitic organisms known so far, to cause relentless damage towards agricultural crops on a global scale. They pierce the roots of host plants and form neo-plastic feeding structures to extract out resources for their functional development. Moreover, they undergo re-differentiation within plant cells to form giant multi-nucleate feeding structures or syncytium. All these processes are facilitated by numerous transcriptomic, proteomic, metabolomic and epigenetic modifications, that regulate different biological attractions among plants and nematodes. Nevertheless, these mechanisms are quite remarkable and have been explored in the present review. Here, we have shed light on genomic as well as genetic approaches to acquire an effective understanding regarding plant-nematode associations. Transcriptomics have revealed an extensive network to unravel feeding mechanism of nematodes through gene-expression programming of target genes. Also, the regulatory circuits of epigenetic alterations through DNA-methylation, non-coding RNAs and histone modifications very well explain epigenetic profiling within plants. Since decades, research have observed many intricacies to elucidate the dynamic nature of epigenetic modulations in plant-nematode attractions. By this review, we have highlighted the functional aspects of small RNAs in inducing plant-nematode parasitism along with the putative role of miRNAs. These RNAs act as chief genetic elements to mediate the expressional changes in plants through post-transcriptional silencing of various effector proteins as well as transcriptional factors. A pragmatic role of miRNAs in modulating gene expression in nematode infection and feeding site development have also been reviewed. Hence, they have been considered master regulators for functional reprogramming the expression during establishment of feeding sites. We have also encapsulated the advancement of genome-broadened DNA-methylation and untangled the nematode mediated dynamic alterations within plant methylome along with assessing transcriptional activities of various genes and transposons. In particular, we have highlighted the role of effector proteins in stimulating epigenetic changes. Finally, we have emerged towards a molecular-based core understanding about plant-nematode associations.

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

Background

Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues.

Results

We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data.

Conclusions

To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07735-7.

Epigenetic Mechanisms in Nematode-Plant Interactions

Epigenetic mechanisms play fundamental roles in regulating numerous biological processes in various developmental and environmental contexts. Three highly interconnected epigenetic control mechanisms, including small noncoding RNAs, DNA methylation, and histone modifications, contribute to the establishment of plant epigenetic profiles. During the past decade, a growing body of experimental work has revealed the intricate, diverse, and dynamic roles that epigenetic modifications play in plant-nematode interactions. In this review, I summarize recent progress regarding the functions of small RNAs in mediating plant responses to infection by cyst and root-knot nematodes, with a focus on the functions of microRNAs. I also recapitulate recent advances in genome-wide DNA methylation analysis and discuss how cyst nematodes induce extensive and dynamic changes in the plant methylome that impact the transcriptional activity of genes and transposable elements. Finally, the potential role of nematode effector proteins in triggering such epigenome changes is discussed.

Non-coding RNAs having strong positive interaction with mRNAs reveal their regulatory nature during flowering in a wild relative of pigeonpea (Cajanus scarabaeoides)

In higher plants, flower development is a result of crosstalk between many factors like photoperiod, vernalization, hormone concentration, epigenetic modification etc. and is also regulated by non-coding RNAs (ncRNAs). In the present study, we are reporting the involvement of long non-coding RNAs (lncRNAs) and miRNAs during the process of flower development in Cajanus scarabaeoides, an important wild relative of pigeonpea. The transcriptome of floral and leaf tissues revealed a total of 1672 lncRNAs and 57 miRNAs being expressed during flower development. Prediction analysis of identified lncRNAs showed that 1593 lncRNAs were targeting 3420 mRNAs and among these, 98 were transcription factors (TFs) belonging to 48 groups. All the identified 57 miRNAs were novel, suggesting their genera specificity. Prediction of the secondary structure of lncRNAs and miRNAs followed by interaction analysis revealed that 199 lncRNAs could interact with 47 miRNAs where miRNAs were acting in the root of interaction. Gene Ontology of the ncRNAs and their targets showed the potential role of lncRNAs and miRNAs in the flower development of C. scarabaeoides. Among the identified interactions, 17 lncRNAs were endogenous target mimics (eTMs) for miRNAs that target flowering-related transcription factors. Expression analysis of identified transcripts revealed that higher expression of Csa-lncRNA_1231 in the bud sequesters Csa-miRNA-156b by indirectly mimicking the miRNA and leading to increased expression of flower-specific SQUAMOSA promoter-binding protein-like (SPL-12) TF indicating their potential role in flower development. The present study will help in understanding the molecular regulatory mechanism governing the induction of flowering in C. scarabaeoides.

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

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in plant defense responses against viral infections. However, there is no systematic understanding of lncRNAs and circRNAs and their competing endogenous RNA (ceRNA) networks in watermelon under cucumber green mottle mosaic virus (CGMMV) stress. Here, we present the characterization and expression profiles of lncRNAs and circRNAs in watermelon leaves 48-h post-inoculation (48 hpi) with CGMMV, with mock inoculation as a control. Deep sequencing analysis revealed 2373 lncRNAs and 606 circRNAs in the two libraries. Among them, 67 lncRNAs (40 upregulated and 27 downregulated) and 548 circRNAs (277 upregulated and 271 downregulated) were differentially expressed (DE) in the 48 hpi library compared with the control library. Furthermore, 263 cis-acting matched lncRNA-mRNA pairs were detected for 49 of the DE-lncRNAs. KEGG pathway analysis of the cis target genes of the DE-lncRNAs revealed significant associations with phenylalanine metabolism, the citrate cycle (TCA cycle), and endocytosis. Additionally, 30 DE-lncRNAs were identified as putative target mimics of 33 microRNAs (miRNAs), and 153 DE-circRNAs were identified as putative target mimics of 88 miRNAs. Furthermore, ceRNA networks of lncRNA/circRNA-miRNA-mRNA in response to CGMMV infection are described, with 12 DE-lncRNAs and 65 DE-circRNAs combining with 22 miRNAs and competing for the miRNA binding sites on 29 mRNAs. The qRT-PCR validation of selected lncRNAs and circRNAs showed a general correlation with the high-throughput sequencing results. This study provides a valuable resource of lncRNAs and circRNAs involved in the response to CGMMV infection in watermelon.

Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

Long non-coding RNAs (lncRNAs) play important roles in the regulation of complex cellular processes, including transcriptional and post-transcriptional regulation of gene expression relevant for development and stress response, among others. Compared to other important crops, there is limited knowledge of cassava lncRNAs and their roles in abiotic stress adaptation. In this study, we performed a genome-wide study of ncRNAs in cassava, integrating genomics- and transcriptomics-based approaches. In total, 56,840 putative ncRNAs were identified, and approximately half the number were verified using expression data or previously known ncRNAs. Among these were 2229 potential novel lncRNA transcripts with unmatched sequences, 250 of which were differentially expressed in cold or drought conditions, relative to controls. We showed that lncRNAs might be involved in post-transcriptional regulation of stress-induced transcription factors (TFs) such as zinc-finger, WRKY, and nuclear factor Y gene families. These findings deepened our knowledge of cassava lncRNAs and shed light on their stress-responsive roles.

A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)

BACKGROUND

Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed.

RESULTS

A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment.

CONCLUSIONS

These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.

Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.