Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.

Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca²⁺]_i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments.

Transcription factors (TFs) are crucial regulators of plant growth, development, and resistance to environmental stresses. However, comprehensive understanding of the roles of TFs in speciation of Orinus, an extreme-habitat plant on the Qinghai-Xizang (Tibet) Plateau, is limited. Here, we identified 52 TF families, including 2125 members in Orinus, by methodically analysing domain findings, gene structures, chromosome locations, conserved motifs, and phylogenetic relationships. Phylogenetic trees were produced for each Orinus TF family using protein sequences together with wheat (Triticum aestivum L.) TFs to indicate the subgroups. The differences between Orinus and wheat species in terms of TF family size implies that both Orinus- and wheat-specific subfamily contractions (and expansions) contributed to the high adaptability of Orinus. Based on deep mining of RNA-Seq data between two species of Orinus, O. thoroldii and O. kokonoricus, we obtained differentially expressed TFs (DETFs) in 20 families, most of which were expressed higher in O. thoroldii than in O. kokonoricus. In addition, Cis-element analysis shows that MYC and G-box elements are enriched in the promoter region of DETFs, suggesting that jasmonic acid (JA) and abscisic acid (ABA) act synergistically in Orinus to enhance the signalling of related abiotic stress responses, ultimately leading to an improvement in the stress tolerance and speciation adaptation of Orinus. Our data serve as a genetic resource for Orinus, not only filling the gap in studies of TF families within this genus but also providing preliminary insights into the molecular mechanisms underlying speciation in Orinus.

LncRNAs, a type of RNAs exceeding 200 nucleotides (nt) and lacking representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth and development processes in plants. While substantial progress has been made in interpreting the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley remains incomplete. To elucidate the coordination of drought stress responses in Tibetan hulless barely by lncRNAs, we analyzed the previously published RNA-seq data from two cultivars of hulless barley, drought-tolerant (Z772) and drought-sensitive (Z013), subjected to varying durations of drought treatment (0, 1, and 5 h). Initially, we identified a total of 2877 lncRNAs through a strict pipeline, of which 2179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the trans-regulatory functions of lncRNAs, we utilized WGCNA and uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring PCGs were co-clustered in key control modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as TFs. Two of these pairs were validated by qRT-PCR in the Tibetan hulless barley cultivar Kunlun 14. These findings suggested that lncRNAs may participate in regulatory networks involved in drought adaptation in Tibetan hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties.

Long noncoding RNAs (lncRNAs), which are a type of RNA exceeding 200 nucleotides and lack representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth processes in plants. While substantial progress has been made in understanding the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley (Hordeum vulgare L. var. nudum) still remain incompletely understood. To elucidate the coordination of drought stress responses by long non-coding RNAs (lncRNAs), a study analyzed previously published RNA sequencing (RNA-seq) data from two cultivars of hulless barley, Z772 (drought-tolerant) and Z013 (drought-sensitive), subjected to varying durations of drought treatment (0, 1, and 5 h). The objective was to determine the expression profiles of long non-coding RNAs (lncRNAs) in hulless barley. Initially, we identified a total of 2,877 lncRNAs, of which 2,179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the trans-regulatory functions of lncRNAs, we uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring protein-coding genes (PCGs) were co-clustered in key regulatory modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as acting as transcription factors (TFs). Two of these pairs were validated by qRT-PCR in the hulless barley cultivar Kunlun 14. These findings suggest that lncRNAs may participate in regulatory networks involved in drought adaptation in hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties.

Mitogen-activated protein kinases 3 and 6 (MPK3/MPK6) are central to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in Arabidopsis, yet the involvement of long noncoding RNAs (lncRNAs, >200 nt) in these pathways is poorly understood. Here, transcriptomic analyses were performed to compare lncRNA and protein-coding gene (PCG) expression profiles in wild-type (WT) and MPK3/MPK6-deficient (MPK6SR) Arabidopsis plants. These plants were inoculated with either Pseudomonas syringae pv. tomato (Pst) DC3000, which elicits both PTI and ETI, or its type III secretion-deficient mutant, Pst DC3000 hrcC⁻, which induces only PTI. RNA sequencing (RNA-seq) analysis of 18 samples identified 1388 known and 70 novel lncRNAs, among which differentially expressed lncRNAs (DElncRNAs) involved in disease resistance were further identified. Using integrative analyses, including weighted gene co-expression network analysis (WGCNA), prediction of lncRNA cis-regulatory targets for PCGs, and validation via reverse transcription-quantitative PCR (RT-qPCR), three core lncRNA-mediated regulatory modules were identified: (i) MPK3/MPK6-dependent PTI and ETI, where lncRNAs amplify signals; (ii) MPK3/MPK6-dependent PTI, where lncRNAs fine-tune basal immunity; and (iii) MPK3/MPK6-independent PTI and ETI, where lncRNAs serve as a backup regulatory network. These modules form a multi-layered immune regulatory network via cis- and trans-regulation and further enable the identification of lncRNA-PCG pairs involved in both regulatory modes. This work enhances the understanding of the molecular mechanisms underlying plant innate immunity.