Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts in Nicotiana tabacum

lncRNA-Encoded Small Peptide Promotes Viral Infection

The small open reading frames (ORFs) embedded in lncRNA have been identified to encode biologically functional peptides in many species. However, the function of lncRNA-encoded small peptides in the plant antiviral response remains unclear. In this study, an lncRNA Talnc54748 was identified, which encodes the small peptide ORF4. Transgenic Nicotiana benthamiana overexpressing ORF4 could enhance wheat yellow mosaic virus (WYMV) infection. RNA-sequencing analysis revealed that many genes in plant hormone signalling and MAPK signalling pathways were reduced in ORF4-overexpressing lines. The function of SAUR21 and MKK2, involved in plant hormone signalling and MAPK signalling pathways, respectively, was investigated by virus-induced gene silencing assay. Silencing SAUR21 or MKK2 in wheat and N. benthamiana enhanced WYMV infection. Transgenic overexpression of ORF4 not only enhanced the accumulation of tobacco mosaic virus (TMV) and tomato mosaic virus (ToMV), but also promoted Phytophthora capsici or Pseudomonas syringae pv. tomato DC3000 infection. Our results demonstrated that an lncRNA-encoded small peptide plays an important role in plant immunity and provides new insights into the roles of this lncRNA-encoded small peptide in the plant antiviral response.

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.

Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response

Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.