Biotic stress response of lncRNAs in plants

Chapter 18 Biotic stress response of lncRNAs in plants Madiha Zaynaba, Mahpara Fatimab, Yasir Sharifc, Muhammad Qasimd, Mehtab Muhammad Aslame, Muhammad Zohaib Afzalb, and Nelam Sajjade a College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, PR China, bCollege of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China, cCollege of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China, dKey Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, PR China, eCollege of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China 18.1 Introduction Some RNAs transcribed from DNA, but not translated into proteins, directly play an important role in the regulation of gene expression. The RNAs that are not translated to proteins are known as noncoding RNAs (ncRNAs). The ncRNAs are categorized into small noncoding RNAs (sncRNAs) and long noncoding RNAs (lncRNAs). The length of sncRNAs usually is less than 200 nt, and these snRNAs are further classified into siRNAs (small interfering RNAs), miRNAs (microRNAs), transacting siRNAs, piwi-interacting RNAs, and natural antisense transcript siRNAs (Rinn and Chang, 2012). Likewise, usually, lncRNAs have a length of more than 200 nt and are divided into three groups depending on protein-coding genes positioned nearby, i.e., long intergenic noncoding RNAs (lincRNAs), long intronic ncRNAs, and natural antisense transcripts (NATs) (Ma et al., 2013). In plants, identification of lncRNAs started in recent years and is not widespread in comparison to other eukaryotes (Zhang et al., 2014; Tyagi et al., 2018). The lncRNAs are likely to be involved in the regulation of the expression of target genes by different molecular mechanisms (Zhu and Wang, 2012). They have also been involved in the posttranscriptional modifications of mRNA. The lncRNAs have a low potential to encode proteins, but they have a role in regulating the expression of target genes during the process of transcription and translation. It is well-documented that lncRNAs in plants play a role in the regulation of complex gene regulatory networks, which are involved in plant developmental processes and stress tolerance (Heo and Sung, 2011). Long Noncoding RNAs in Plants: Roles in development and stress https://doi.org/10.1016/B978-0-12-821452-7.00018-0 © 2021 Elsevier Inc. All rights reserved. 279 280 Long noncoding RNAs in plants: Roles in development and stress Thousands of lncRNAs have been discovered through in silico predictions and applied tilling arrays at the whole genome and RNA-sequencing (RNASeq) levels in different plant species, including Arabidopsis thaliana (Liu et al., 2012), Zea mays (Li et al., 2014), Triticum aestivum (Xin et al., 2011; Shumayla et al., 2017), Oryza sativa (Zhang et al., 2014), Cucumis sativus (Hao et al., 2015), and Medicago truncatula (Wen et al., 2007). Most of the reported lncRNAs are stress-responsive (Shafiq et al., 2016), e.g., 1212 unique candidate lncRNAs with 309 differentially expressed lncRNAs were predicted under control as well as under Pi starvation in Arabidopsis (Yuan et al., 2016). The 1113 lincRNAs and 17 linTARs (involved in defense) discovered through strand-specific RNA-sequencing in potato were reactive to Pectobacterium carotovorum subsp. brasiliense damage (Kwenda et al., 2016). Similarly, 1565 lncRNAs have been identified in tomato, responsive to TYLCV (tomato yellow leaf curl virus) infestation (Wang et al., 2015). However, the limited knowledge is available about the regulation of lncRNAs under stresses at the molecular level, except a few have been functionally studied. Two different lncRNAs in Arabidopsis, i.e., COLDAIR and COOLAIR, have been documented to be involved in the silencing of FLC (FLOWERING LOCUS C) at transcription in vernalization process via chromatin modifications (Swiezewski et al., 2009). During the recent past, an antisense and unpolyadenylated lncRNA (ASL) was identified that plays various roles in the silencing of FLC (Shin and Chekanova, 2014). Moreover, IPA1 lncRNA is induced by Pi starvation, which plays a role as miR399 target mimic and leads to reduced cleavage of PHO mRNA mediated by miR399 (Franco-Zorrilla et al., 2007). 18.2 Long noncoding RNAs and plant defense mechanism The antiviral defense in plants involves two key mechanisms. Firstly, RNA silencing is mediated by double-stranded viral RNA that is processed by RNA silencing system of a host into siRNAs of 21–24 nt, which in turn is involved in RNA degradation through homology-dependent manner (Szittya and Burgyán, 2013). Viruses overcome this defense response through the expression of suppressors of RNA silencing that affects various steps of this defense system (Csorba et al., 2015). A few also produce ncRNAs which generate a high amount of viral siRNAs that act as a sponge for host components of RNA silencing system, and hence, inhibit the degradation of other RNA species of virus, e.g., CaMV35S, and 8S RNA (Hohn, 2015). Secondly, phytohormones, e.g., salicylic acid (SA) and 2-hydroxybenzoic acid, are involved in signaling pathways. For instance, SA is a multifaceted hormone and involved in various plant developmental processes and response to stresses (Miura and Tada, 2014). It has demonstrated that SA participates in signal transduction activating plant defense system, resulting in the suppression of viral movement and amplification (Lee et al., 2016). The perception of pathogen induces SA, Biotic stress response of lncRNAs in plants Chapter | 18 281 which leads to the activation of responsive genes involved in the defense system, including those encoding the PR (pathogenesis-related) proteins (Alazem and Lin, 2015). Some viruses produce different proteins that hinder SA signaling (Love et al., 2012). However, so far, no studies described the role of lncRNAs produced by the virus, mitigating the SA-regulated pathways. The phytoplasma-infected plants can make effective strategies to protect themselves from invasion (Hegenauer et al., 2016). First, phytoplasma’s presence is perceived by plants via PAMPs (pathogen-associated molecular patterns), which produce resistance. At this stage, plants generate a high quantity of ROS (reactive oxygen species) as well as antitoxin, which activate a hypersensitive response. Besides, few effectors, e.g., TENGU and SAP, are secreted by phytoplasmas via the general secretory system (Sec secretion system), which influences the host PAMP-activated defense signal transduction and increases colonization effectively as well as assist in their multiplication in the host plant cells. Plants recognize effectors by utilization of cellular receptor proteins, which results in activation of the immune response and finally involves activation of MAPK cascades as well as induction of disease-resistant protein. The immune responses of the plant to phytoplasma infestation were activated and responsive genes that encode enzymes for signaling pathways, e.g., PERK1 (proline-rich receptor-like protein kinase), and important marker genes convoluted in the related processes (e.g., disease-resistant protein, SRC protein, and glucan endo-1,3-beta-glucosidase) were identified. The concentration of glucan endo-1,3-beta-glucosidase enhanced distinctly in the tobacco infected with necrotizing viruses (Beffa et al., 1993). Likewise, the gene-encoding SRC2 was highly expressed in infected peppers with Xanthomonas axonopodis pv. glycines (Kim et al., 2008). Remarkably, the upregulation of PERK1, glucan endo-1,3-beta-glucosidase, disease-resistant protein, and SRC2 protein was noticed in infested cuttings with phytoplasma. Also, the upregulation of genes encoding-resistant proteins against diseases has been reported, when infected with phytoplasma in an earlier study in Paulownia, while three lncRNAs, including TCONS_00021207, TCONS_00026765, and TCONS_00034613, were expected to control the expression levels of vital genes which encode diseaseresistant protein, SRC2 protein, and glucan endo 1, 3-betaglucosidase, respectively. Therefore, these lncRNAs mentioned above possibly have important roles in phytoplasma-infected cuttings. Additionally, the expression level of gene-encoding cytochrome P450 also increased in the PTI cuttings. As an oxidant, cytochrome P450 can remove excess ROS and prevent cell damage. In the earlier study, Paulownia plants infected with phytoplasma showed an elevated level of the cytochrome. The infected cuttings with phytoplasma displayed downregulation of TCONS_00031692 and upregulation of TCONS_00007939; both of these regulate the expression of cytochrome P450-encoding gene (LCONS_00023050). Therefore, lncRNAs might be significantly involved in hypersensitive response against ROS and effector-activated immunity inside phytoplasma-infected cuttings. 282 Long noncoding RNAs in plants: Roles in development and stress It has described that co-expressed and co-localized transcripts can anticipate the possible lncRNA functions (Wilusz et al., 2009). The cis examination indicated high consequence with GO terms linked to morphological variations such as structural cell wall constituents, the metabolic process of chitin, the catabolic process of chitin, as well as macromolecule metabolic process of cell wall, among others. In plants, the cell wall acts as the first hurdle against pathogen attack and is mainly composed of proteins, polysaccharides, and aromatic polymers (Underwood and Somerville, 2008). The perception of fungal chitin via host plants is crucial for activating PAMP- initiated immunity (PTI) against fungal attack (Kombrink et al., 2011). 18.3 Identification of lncRNAs related to biotic stress One study conducted on Brassica napus identified a total of 3181 lncRNA comprising intergenic (2821), antisense (111), exonic overlap (76), and lncRNA isoforms (173). Moreover, 41 lncRNAs are recognized as the originators of miRNA constituting miRNA156, miRNA169, and miRNA394. These miRNAs showed a prominent role in regulating plant responses against fungal pathogens (Joshi et al., 2016). A total of 931 lncRNAs have been recognized in response to Sclerotinia sclerotiorum, and 12 lncRNAs have been used to validate their expression using qRT-PCR that revealed different expressions (Joshi et al., 2016). Two genotypes of grapevine-susceptible (Cabernet Franc.) and -resistant (Merlot) infected with Lasiodiplodia theobromae were used to perform high-throughput RNA-Seq. Inclusively, it was anticipated that a total of 1826 lncRNAs were present along with intergenic lncRNA and antisense RNA transcripts (Xing et al., 2019). Hevea brasiliensis leaves infected with Colletotrichum gloeosporioides at different stages showed that dominant lncRNAs are involved in response to infection. The outcome showed that the function of lncRNA 11,205 recruiting TF (transcription factor) and other lncRNA11041 and incRNA11205 probably triggers the assembly of several disease-responsive miRNAs (Yin et al., 2019). Susceptible and tolerant banana genotypes were sequenced through the Illuminasequencing tool for recognition of differential expression under both control and stressed environments. The resulting sequence was assembled into 201,256 and 172,434 transcriptional units for Pratylenchus coffeae and Mycosphaerella eumusae, respectively (Muthusamy et al., 2019). A total of 5142 lncRNAs comprising 3031 and 1672 intergenic and 440 antisense were acknowledged in both resistant and susceptible banana genotypes. Furthermore, lncRNA 1250 and 1284 were contrastingly expressed in response to P. coffeae, and M. eumusae, respectively (Muthusamy et al., 2019). The interaction between lncRNA and mRNA regulates the suppression of Horcolin protein (antifungal protein) accountable for ELSD sensitivity in banana genotypes (Muthusamy et al., 2019). LncRNA 1331 exhibited differential expression, GO (gene ontology), and KEGG analysis which demonstrated that various protein-encoding lncRNAs were reinforced under stressed conditions. Additionally, 55 lncRNAs out of Biotic stress response of lncRNAs in plants Chapter | 18 283 8414 were expected as a mimic of cotton miRNA 285. Quantitative real-time PCR (qPCR) proved that all lncRNAs were related to aphid infection (Zhang et al., 2019). Recently, one study characterized the lncRNAs of two main lignindegrading basidiomycetes, Coniophora puteana and Serpula lacrymans, with 2712 and 2242 lncRNAs, respectively, majorly originating from intergenic regions in respective species (Borgognone et al., 2019). Previous studies specified Phytophthora infestans disease-resistant tomato varieties produced using WRKY1 (transcription factor). However, the mechanism underlying WRKY1 arbitrating resistance remains poorly understood. Wild-type and WRKY1 overexpressing tomato lines are used to identify contrastingly expressed genes and lncRNAs and also investigated gene networks of long noncoding RNA. The outcomes of promoter-GUS fusion and yeast hybrid assay exhibited the upregulation of lncRNA33732 by WRKY1 (Cui et al., 2019). A set of lncRNAs recognized and characterized in animals, fungi, and plants played an essential role in biological mechanisms. But, minimal information is available on its role in oomycete phytopathogens, which leads to catastrophic loss to the ecosystems (Wang et al., 2018a). Phytophthora sojae oomycete phytopathogen is used to identify specific RNA transcript sequencing; a total of 940 lncRNA along with 1010 isoforms were found to have shorter nucleotide length, larger exon length, the smaller number of exons, fewer GC%, and higher minimal energy contrasting with protein-encoding genes. RNA-Seq data disclose an interaction among transcript of lncRNAs and adjacent genes coding effector proteins (Wang et al., 2018c). Strand-specific RNA-Seq of susceptible and resistant banana cultivars, infected with Fusarium oxysporum, specified 5294 lncRNAs with high confidence provided with strict filtration along with intergenic and antisense lncRNA (Li et al., 2017). F. oxysporum and mock-inoculated-susceptible and resistant cultivars also revealed some differentially expressed lncRNAs (Li et al., 2017). Kang et al. (2019) focused on the discovery of functional identification and characterization of plant important lincRNAs after the viral infection. This discovery was promoted through transcriptome analysis by using RNA-Seq analysis (Kang et al., 2019). Inoculated neutron irradiated tomato seeds with tomato yellow leaf curl virus (TYLCV) and performed RNA-Seq to find out the lncRNAs. With the help of bioinformatics analysis, they found a total of 1563 lncRNAs, half of which were originated from intergenic regions and 35% were antisense lncRNAs. Almost 794 lncRNAs were functionally associated with binding function, showed attraction with other molecules, and localized in membrane and cytosol of the cell (Zhou et al., 2019). Another study conducted on potato (Solanum tuberosum) stem tissues identified 1113 long intergenic ncRNAs through strand-specific RNA-Seq. The size of expressed lincRNAs in all 12 chromosomes was smaller than protein-coding genes, and only a single exon was present similar to other studied plants. Further timecourse RNA-Seq analysis revealed that 559 lincRNAs were responsive to P. carotovorum subsp. brasiliense, and 17 lincRNAs out of these 559 were linked with 12 defense genes (Kwenda et al., 2016). Whole-transcriptome RNA-Seq of 284 Long noncoding RNAs in plants: Roles in development and stress 6-h aphid damaged cotton plants identified 8414 lncRNAs, mainly belonging to intergenic regions, i.e., 77%, where 10% was sense lncRNAs, 7% antisense, and 4% intronic lncRNAs. Further, 1331 lncRNAs showed differential expression, while KEGG pathway and GO analysis showed that many target genes of these lncRNAs were stress-responsive (Zhang et al., 2019). 18.4 Long noncoding RNAs as front-line player against pathogens Canola is an important crop, and its seed contains almost 45% oil content. Canola production is mainly affected globally due to Sclerotinia stem rot disease caused by a pathogenic fungus (S. sclerotiorum). When plants encounter any environmental stress (biotic/abiotic), they evolve a different mechanism to cope with that particular stress. LncRNA plays a vital role in driving gene expression. Limited information is available on their identification and function in some plant species. Antisense lncRNA (TCONS-00000966) from B. napus presents 90% overlapping with defensin genes, which suggests its interaction in regulating defense-related genes upon S. sclerotiorum infection. These findings elaborate on the prospective involvement of lncRNAs in driving expression of those genes expressed under biotic stress (Joshi et al., 2016). 18.4.1 Role against fungi Recently, several lncRNAs appeared as important regulators of biological mechanisms in both plants and animals, involving response against biotic and abiotic stress. Upon infection of L. theobromae, various lncRNAs were expected to be originators for grapevine miRNA. These findings open new insights into grapevine lncRNAs, which are involved in response to L. theobromae infection (Xing et al., 2019). Developing disease-resistant crops is a difficult challenge for all plant species, while the probable function of lncRNA against fungal infection remains unknown. In another study, Gossypium barbadense’s highly susceptible, susceptible, highly tolerant, and super highly tolerant recombinant inbred lines (RILs) along with their resistant and susceptible parents were infected with F. oxysporum, and their responses were compared. It was observed that aside from fungal susceptibility, the expression of infection-induced genes was remarkably increased in disease-resistant plant pathways. However, the expression of lncRNAs induced by F. oxysporum infection was significantly related to plant susceptibility. Bioinformatics analysis also evidenced that F. oxysporumregulated lncRNAs were significantly enriched in disease-resistant-related plant pathway involving glycolysis, phytohormonal signaling pathway, glutathione metabolism, butanoate metabolism, and anthocyanin biosynthesis. Collectively, these findings propose that lncRNA would play a vital role in response to pathogenic fungi as well as in the development of disease-resistant recombinant lines (Yao et al., 2019). H. brasiliensis (Rubber tree) is an important economic plant, Biotic stress response of lncRNAs in plants Chapter | 18 285 and anthracnose is a common disease predominantly caused by fungus C. gloeosporioides, which decrease rubber production. Whether this disease comprises noncoding RNAs or lncRNAs remains unclear. However, the development of disease-resistant varieties would be a positive and significant step toward the green revolution globally. In the last few years, considerable progress was made on identifying genes involved in disease-resistant/tolerance. Experimental and computational findings cleared that dominant lncRNAs are involved in response to pathogenic fungi (Yin et al., 2019). A study reported the disease-responding mechanism of lncRNA against the attack of Verticillium dahliae in cotton. It showed that induced lncRNAs indicate a biased expression pattern in allotetraploid cotton. Bioinformatics and other comparative analyses proposed distinct response mechanisms of G. barbadense cv. 7124 (resistant) and Gossypium hirsutum cv. YZ1 (susceptible). Moreover, functional examination indicated that GhlncNAT-ANX2 and GhlncNAT-RLP7 (2-core lncRNAs)-silenced seedling exhibited an improved tolerance against Botrytis cinerea and V. dahliae probably linked with enhanced expression of LOXA and LOX2 (Zhang et al., 2018). Aside from the role of lncRNAs in various plant developmental processes, the mechanism underlying their response to disease remains unanswered. For assessing the defense role of long nonprotein-coding RNAs (npcRNAs), two wheat genotypes (susceptible JD8, resistant JD8-pm30) were infected with powdery mildew disease caused by Blumeria graminis. Sequencing analysis revealed that a set of long npcRNAs were expressed differentially. Interestingly, expression pattern was the same in both susceptible and resistant genotypes. For example, TalnRNA5, TalnRNA9, TapmlnRNA19, and TapmlnRNA30 were upregulated, while TalnRNA21 downregulated. Furthermore, the expression of all long npcRNAs was tissue-specific, i.e., TapmlnRNA30 was induced in seed, TalnRNA5 in all tissues, and TalnRNA9 expressed in seed, root, and leaf. These results support the contribution of long npcRNAs in defense mechanism, even though the molecular basis is still unidentified (Xin et al., 2011). 18.4.2 Role against nematode Researchers attempted to recognize novel lncRNAs, responsive to M. eumusae, which cause eumusae leaf spot disease and nematode P. coffeae, causing rootlesions. P. coffeae infection identified 5615 lncRNAs from susceptible and resistant cultivars of banana. The study also revealed 1284 and 1250 differentially expressed lncRNAs against P. coffeae and M. eumusae. Moreover, 100 lncRNA played a vital role in numerous developmental processes and drought stress responses in banana (Muthusamy et al., 2019). 18.4.3 Role against viruses Citrus tristeza virus (CTV) belongs to the Closterovirus genus, which potentially caused economic lose in citrus plants and produces subgenomic noncoding 286 Long noncoding RNAs in plants: Roles in development and stress RNAs called LMT1 (low-molecular-weight tristeza 1), previously considered to be CTV replication by-product (Kang et al., 2019). The investigations of a nonLMT1 producing variant of CTV to study the possible role of LMT1 in the viral infection cycle revealed that absence of LMT1 did not affect the viral replication and virions formation. On the other hand, the study demonstrated that mutant of viruses was significantly reduced, spreading tendency in Nicotiana benthamiana and establishing inability in citrus. The herbaceous host introduced with CTV-LMT1d showed that SA and SA-related pathogenic genes were upregulated as compared to herbaceous host inoculated with wild-type virus (CTV-WT). Furthermore, the study revealed that LMT1 RNA produced by ectopic expression or CTV-WT upregulated alternative oxidative genes and suppressed SA accumulation to moderate ROS accumulation in N. benthamiana leaves (Kang et al., 2019). LncRNAs’ function during DNA virus infection in tomatoes was assessed through RACE technique by using three replicates. Generally, predicted data presented that 1565 lncRNAs, including both antisense transcripts and long intergenic RNAs, were involved in TYLCV infection through VIGS (virusinduced gene silencing). The study trial verified the lncRNA-associated function, differentially observed between 0 and 7 dpi (days postinoculation). LncRNAs also act as CeRNAs (competing endogenous RNAs), which regulated the RNA transcripts by competing for endogenous target mimics (eTMs) TYLCV infection-causing microRNAs in tomatoes. These findings gave a new direction about lncRNAs’ involvement in response to virus infection, including TYLCV in tomatoes (Wang et al., 2015). Two major viruses with wide geographical distribution affected the tomatoes’ economy, and worldwide disease spread is begomoviruses and TYLCV. Research reports present that noncoding RNAs’ interaction after TYLCV infection in tomatoes helped to elucidate the mechanism of TYLCV development. TYLCV contains ssDNA circular genome and noncoding intergenic region (IR), which mediated viral DNA replication in host cells, but still no research work is available related to the direct involvement of TYLCV in host disease development. During infection, some phenotypic abnormalities can be observed, which demonstrated intergenic region-oriented protein-coding regions to promote the viral genome replication. IR sequence contains 25 nt segments, which are complementary to lncRNA designated as SILNR1 in TYLCV-susceptible tomatoes, and 14 nt deletion in 25 nt intergenic region, but do not show any resistance. For the silencing induction derived viral small interfering RNAs (shRNAs) with 25 nt intergenic region (SILNR1 downregulated) were associated with TYLCV evocative symptoms such as curled and stunted leaves. Obtained results suggested that lncRNAs interact with shRNAs to control infection. On the other hand, consistency promotes virus development; if overexpressed SILNR1, then it reduced TYLCV accumulation. Additionally, SILNR1 silencing without virus infection induces TYLCV leaf-like phenotype. Experimental results described the host lncRNAs and viral sRNAs’ relation that is unknown and help to provide Biotic stress response of lncRNAs in plants Chapter | 18 287 a conceptual model to understand the disease induction and host immunity relation and effective strategies to control pathogenicity caused by TYLCV virus (Yang et al., 2019). Plant initiated immune response on the recognition followed by pathogen-associated recognition, and molecular-related patterns include elf18, in the past identified in Arabidopsis with ELF18-induced lncRNA1 (ELENA1), which act as a positive immune gene transcriptional regulation and, when associated with MED19a (Mediator subunit 19a), help to enhance the PR1 (Pathogenesis-related genes) complex promoter. In vitro and in vivo experiments presented that ELENA1 can interact with FIB2 (Fibrillarin 2). Bimolecular and co-immunoprecipitation fluorescence assay showed that FIB2 directly interacts with MED19a at specific locations such as nucleolus and nucleoplasm. Fib2 mutant analysis presented that FIB2 (PRI) acts as a negative regulator for genes responsible for immunity. The biochemical and genetic analysis proposed that ELENA1 has the ability to dissociate the FIB2 + MED19a complex and move out FIB2 from promoter PR1 and enhance its expression, which was increased by evicting FIB2 repressor from the MED19a activator. Study findings were exposed to transcriptional complexities to regulate the immune-related genes with the relation of long noncoding RNAs in plants (Seo et al., 2019). 18.4.4 Role against bacteria Long noncoding RNAs, a class of noncoding RNAs, were implicated for gene regulation and expression both in plants and mammals, while most studies in mammals determine the biological processes, but the lncRNAs’ functions in plants were still under study. Exclusively, long intergenic noncoding RNAs play defense roles in plants. These results proposed that lincRNAs have potential defense roles and this work also provides first lincRNAs library and novel lncRNAs of potato defense in response to P. carotovorum subsp. brasiliense, which was a member of soft rot phytopathogens known as Enterobacteriaceae (Kwenda et al., 2016). Another fatal disease PaWB (Paulownia witches broom) caused substantial economic losses. Long noncoding RNAs have played a substantial regulatory role in transcriptional and posttranscriptional regulatory pathways. Against this phytoplasma disease (PaWB), the identification of significant lncRNAs and vital roles of lncRNAs were poorly characterized. For that purpose, it was needed to perform RNA-Seq analysis on healthy Paulownia tomentosa and PaWB-infected P. tomentosa, treated with 100 mg/L rifampicin. After analysis, total 28,614 distinctive mRNAs and 3693 potential long noncoding RNAs were obtained. However, when compared to the coding genes and lncRNAs, comparison designated that lncRNAs have shorter transcripts and fewer exons and demonstrated substantial expression specificity. 18.4.5 Role against insects According to the comparison scheme, identified PaWB-associated 1063 mRNAs and 110 lncRNAs, the data identification characterized that 9 288 Long noncoding RNAs in plants: Roles in development and stress PaWB-related lncRNAs regulated 12 PaWB-related target genes (Wang et al., 2018b). For significant lncRNAs, functions were studied in different plants, while the functions of lncRNAs on cotton crops were rarely unknown under aphids (Aphis gossypii Glover) attack. For this purpose, whole RNAs transcriptome sequence analysis was performed on leaves at four-leaf stage (G. hirsutum, ZM-03199) and damaged at different stages (including 0, 6, 12, 24, 48, and 72 h) affected by cotton aphids. Molecular analysis by RT-qPCR revealed that all selected lncRNAs were comparative to aphid damage. These results provide a solid foundation for cotton lncRNAs’ functions against aphids damage (Zhang et al., 2019). Recently, long noncoding RNAs become a scientist’s interest due to their significant biological roles. The genome-wide characterization and identification of reputed lncRNAs in global insect (pest) called Plutella xylostella. During the development of diamondback moth (DBM), expression profiling presented 114 lncRNAs’ expression in which the majority were temporally specified. However, the biological function was uncharacterized in lncRNAs in which many are ceRNAs and mi-RNAs precursors directly involved in miRNAs regulatory pathways. This study has importance for valuable information on further molecular-based analysis for BDM development and provides the foundations for lncRNAs’ discovery function in P. xylostella (Wang et al., 2018c). 18.5 Conclusions Association of long noncoding RNAs with plant immunity and dealing with pathogen virulence attract researchers to exploit RNA silencing machinery in terms of augmented plant immunity against diseases. Although considerable efforts are under progress to recognize the protection mechanism of plant lncRNAs, the precise antipathogenic defense part of their function is still vague. Similarly, lncRNAs are not getting large-scale attention for their utility in antimicrobial immunity. As it is known that pathogens have enhanced their virulence by developing lncRNAs, further studies aiming pathogen lncRNAs and the virulence development can help researchers in decoding plant-pathogen interactions. Finding missing gaps in infection-mediated lncRNAs production can be beneficial. We expect that further research on lncRNAs-mediated plant defense against different diseases, by achieving disease resistance, will help us to improve global food security. References Alazem, M., Lin, N.S., 2015. Roles of plant hormones in the regulation of host–virus interactions. Mol. Plant Pathol. 16, 529–540. Beffa, R.S., Neuhaus, J.-M., Meins, F., 1993. Physiological compensation in antisense transformants: specific induction of an “ersatz” glucan endo-1, 3-beta-glucosidase in plants infected with necrotizing viruses. PNAS 90, 8792–8796. Borgognone, A., Sanseverino, W., Aiese Cigliano, R., Castanera, R., 2019. Distribution, characteristics, and regulatory potential of long noncoding RNAs in brown-rot fungi. Int. J. Genomics 2019. Biotic stress response of lncRNAs in plants Chapter | 18 289 Csorba, T., Kontra, L., Burgyán, J., 2015. Viral silencing suppressors: tools forged to fine-tune hostpathogen coexistence. Virology 479, 85–103. Cui, J., Jiang, N., Meng, J., Yang, G., Liu, W., Zhou, X., et al., 2019. LncRNA33732‐respiratory burst oxidase module associated with WRKY1 in tomato‐Phytophthora infestans interactions. Plant J. 97, 933–946. Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., et al., 2007. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39, 1033. Hao, Z., Fan, C., Cheng, T., Su, Y., Wei, Q., Li, G., 2015. Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber. PLoS One 10, e0121800. Hegenauer, V., Fürst, U., Kaiser, B., Smoker, M., Zipfel, C., Felix, G., et al., 2016. Detection of the plant parasite Cuscuta reflexa by a tomato cell surface receptor. Science 353, 478–481. Heo, J.B., Sung, S., 2011. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331, 76–79. Hohn, T., 2015. RNA based viral silencing suppression in plant pararetroviruses. Front. Plant Sci. 6, 398. Joshi, R.K., Megha, S., Basu, U., Rahman, M.H., Kav, N.N., 2016. Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus. PLoS One 11, e0158784. Kang, S.H., Sun, Y.D., Atallah, O.O., Huguet-Tapia, J.C., Noble, J.D., Folimonova, S.Y., 2019. A long non-coding RNA of Citrus tristeza virus: role in the virus interplay with the host immunity. Viruses 11 (5), 436. Kim, M.I., Kim, H.S., Jung, J., Rhee, S., 2008. Crystal structures and mutagenesis of sucrose hydrolase from Xanthomonas axonopodis pv. glycines: insight into the exclusively hydrolytic amylosucrase fold. J. Mol. Biol. 380, 636–647. Kombrink, A., Sanchez-Vallet, A., Thomma, B.P., 2011. The role of chitin detection in plant– pathogen interactions. Microbes Infect. 13, 1168–1176. Kwenda, S., Birch, P.R., Moleleki, L.N., 2016. Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. BMC Genomics 17, 614. Lee, W.S., Fu, S.F., Li, Z., Murphy, A.M., Dobson, E.A., Garland, L., et al., 2016. Salicylic acid treatment and expression of an RNA-dependent RNA polymerase 1 transgene inhibit lethal symptoms and meristem invasion during tobacco mosaic virus infection in Nicotiana benthamiana. BMC Plant Biol. 16, 15. Li, L., Eichten, S.R., Shimizu, R., Petsch, K., Yeh, C.T., Wu, W., et al., 2014. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol. 15, R40. Li, W., Li, C., Li, S., Peng, M., 2017. Long noncoding RNAs that respond to Fusarium oxysporum infection in ‘Cavendish’ banana (Musa acuminata). Sci. Rep. 7, 16939. Liu, J., Jung, C., Xu, J., Wang, H., Deng, S., Bernad, L., et al., 2012. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24, 4333–4345. Love, A.J., Geri, C., Laird, J., Carr, C., Yun, B.W., Loake, G.J., et al., 2012. Cauliflower mosaic virus protein P6 inhibits signaling responses to salicylic acid and regulates innate immunity. PLoS One 7, e47535. Ma, L., Bajic, V.B., Zhang, Z., 2013. On the classification of long non-coding RNAs. RNA Biol. 10, 924–933. Miura, K., Tada, Y., 2014. Regulation of water, salinity, and cold stress responses by salicylic acid. Front. Plant Sci. 5, 4. 290 Long noncoding RNAs in plants: Roles in development and stress Muthusamy, M., Uma, S., Suthanthiram, B., Saraswathi, M.S., Chandrasekar, A., 2019. Genomewide identification of novel, long non-coding RNAs responsive to Mycosphaerella eumusae and Pratylenchus coffeae infections and their differential expression patterns in diseaseresistant and sensitive banana cultivars. Plant Biotechnol. Rep. 13, 73–83. Rinn, J.L., Chang, H.Y., 2012. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166. Seo, J.S., Diloknawarit, P., Park, B.S., Chua, N.H., 2019. ELF18‐INDUCED LONG NONCODING RNA 1 evicts fibrillarin from mediator subunit to enhance PATHOGENESIS‐RELATED GENE 1 (PR1) expression. New Phytol. 221, 2067–2079. Shafiq, S., Li, J., Sun, Q., 2016. Functions of plants long non-coding RNAs. Biochim. Biophys. Acta (BBA)-Gene Regul. Mech. 1859, 155–162. Shin, J.-H., Chekanova, J.A., 2014. Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis. PLoS Genet. 10, e1004612. Shumayla, Sharma, S., Taneja, M., Tyagi, S., Singh, K., Upadhyay, S.K., 2017. Survey of high throughput RNA-seq data reveals potential roles for lncRNAs during development and stress response in bread wheat. Front. Plant Sci. 8, 1019. Swiezewski, S., Liu, F., Magusin, A., Dean, C., 2009. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799. Szittya, G., Burgyán, J., 2013. RNA interference-mediated intrinsic antiviral immunity in plants. In: Intrinsic Immunity. Springer, pp. 153–181. Tyagi, S., Sharma, A., Upadhyay, S.K., 2018. Role of next-generation RNA-Seq data in discovery and characterization of long non-coding RNA in plants. In: Çiftçi, Y.Ö. (Ed.), Next Generation Plant Breeding. IntechOpen. https://doi.org/10.5772/intechopen.72773. Underwood, W., Somerville, S.C., 2008. Focal accumulation of defences at sites of fungal pathogen attack. J. Exp. Bot. 59, 3501–3508. Wang, J., Yu, W., Yang, Y., Li, X., Chen, T., Liu, T., et al., 2015. Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection. Sci. Rep. 5, 16946. Wang, Y., Xu, T., He, W., Shen, X., Zhao, Q., Bai, J., et al., 2018a. Genome-wide identification and characterization of putative lncRNAs in the diamondback moth, Plutella xylostella (L.). Genomics 110, 35–42. Wang, Y., Ye, W., Wang, Y., 2018b. Genome‐wide identification of long non‐coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae. Mol. Plant Pathol. 19, 2177–2186. Wang, Z., Li, B., Li, Y., Zhai, X., Dong, Y., Deng, M., et al., 2018c. Identification and characterization of long noncoding RNA in Paulownia tomentosa treated with methyl methane sulfonate. Physiol. Mol. Biol. Plants 24, 325–334. Wen, J., Parker, B.J., Weiller, G.F., 2007. In silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biol. 7, 485–505. Wilusz, J.E., Sunwoo, H., Spector, D.L., 2009. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23, 1494–1504. Xin, M., Wang, Y., Yao, Y., Song, N., Hu, Z., Qin, D., et al., 2011. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol. 11, 61. Xing, Q., Zhang, W., Liu, M., Li, L., Li, X., Yan, J., 2019. Genome-wide identification of long non-coding RNAs responsive to Lasiodiplodia theobromae infection in grapevine. Evol. Bioinforma. 15. 1176934319841362. Biotic stress response of lncRNAs in plants Chapter | 18 291 Yang, Y., Liu, T., Shen, D., Wang, J., Ling, X., Hu, Z., et al., 2019. Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms. PLoS Pathog. 15, e1007534. Yao, Z., Chen, Q., Chen, D., Zhan, L., Zeng, K., Gu, A., et al., 2019. The susceptibility of sea-island cotton recombinant inbred lines to Fusarium oxysporum f. sp. vasinfectum infection is characterized by altered expression of long noncoding RNAs. Sci. Rep. 9, 2894. Yin, H., Zhang, X., Zhang, B., Luo, H., He, C., 2019. Revealing the dominant long noncoding RNAs responding to the infection with Colletotrichum gloeosporioides in Hevea brasiliensis. Biol. Direct 14, 7. Yuan, J., Zhang, Y., Dong, J., Sun, Y., Lim, B.L., Liu, D., et al., 2016. Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 17, 655. Zhang, Y.C., Liao, J.Y., Li, Z.Y., Yu, Y., Zhang, J.P., Li, Q.F., et al., 2014. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol. 15, 512. Zhang, L., Wang, M., Li, N., Wang, H., Qiu, P., Pei, L., et al., 2018. Long noncoding RNA s involve in resistance to Verticillium dahliae, a fungal disease in cotton. Plant Biotechnol. J. 16, 1172–1185. Zhang, J., Yang, Z., Feng, P., Zhong, X., Ma, Q., Su, Q., et al., 2019. Identification and the potential roles of long non-coding RNAs in cotton leaves damaged by Aphis gossypii. Plant Growth Regul. 88, 215–225. Zhou, Y., Cho, W.K., Byun, H.S., Chavan, V., Kil, E.J., Lee, S., et al., 2019. Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus. PeerJ 7, e6286. Zhu, Q.H., Wang, M.B., 2012. Molecular functions of long non-coding RNAs in plants. Genes 3, 176–190.