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

• Published in: Non-coding RNA 2023-08, Vol.9 (5), p.48
• Main Authors: Hidalgo, Manuel, Ramos, Cynthia, Zolla, Gaston
• Format: Article
• Language: English
• Subjects: Algorithms; Andean lupin; Annotations; Conservation; Cytoplasm; Drought; Drought resistance; Exosomes; Flowers & plants; Genes; Homology; Identification; legume; Legumes; lncRNA; Lupinus mutabilis; Malnutrition; MicroRNAs; Non-coding RNA; Protein structure; SECIS-like element; Secondary structure; Transcriptomics
• ISSN: 2311-553X; 2311-553X
• DOI: 10.3390/ncrna9050048

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.