Bridging the Gap: Combining Genomics and Transcriptomics Approaches to Understand Stylosanthes scabra, an Orphan Legume from the Brazilian Caatinga

• Published in: Plants (Basel) Vol. 12; no. 18; p. 3246
• Main Authors: Ferreira-Neto, José Ribamar Costa, da Silva, Manassés Daniel, Binneck, Eliseu, de Melo, Natoniel Franklin, da Silva, Rahisa Helena, de Melo, Ana Luiza Trajano Mangueira, Pandolfi, Valesca, Bustamante, Fernanda de Oliveira, Brasileiro-Vidal, Ana Christina, Benko-Iseppon, Ana Maria
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 13.09.2023; MDPI
• Subjects: Adaptation; aquaporins; Arid environments; Biological activity; Biosynthesis; Drought; Extreme environments; Fertility; Flow cytometry; Flowers & plants; Gene clusters; Gene families; Genes; Genomes; Genomic analysis; Genomics; Legumes; Metabolic pathways; mobile elements; Morphology; nuclear genome; Physiology; Proteins; Proteomes; PRR-genes; Quantitative trait loci; R-genes; Rain; Ribosomal DNA; Rust fungi; Salinity; Semi arid environments; Semiarid environments; Soybeans; Stylosanthes scabra; Terpenes; Transcriptomics; Water deficit; Brazil
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12183246

Stylosanthes scabra is a scientifically orphaned legume found in the Brazilian Caatinga biome (a semi-arid environment). This work utilized omics approaches to investigate some ecophysiological aspects of stress tolerance/resistance in S. scabra, study its genomic landscape, and predict potential metabolic pathways. Considering its high-confidence conceptual proteome, 1694 (~2.6%) proteins were associated with resistance proteins, some of which were found in soybean QTL regions that confer resistance to Asian soybean rust. S. scabra was also found to be a potential source of terpenes, as biosynthetic gene clusters associated with terpene biosynthesis were identified in its genome. The analysis revealed that mobile elements comprised approximately 59% of the sequenced genome. In the remaining 41% of the sections, some of the 22,681 protein-coding gene families were categorized into two informational groups: those that were specific to S. scabra and those that expanded significantly compared to their immediate ancestor. Biological process enrichment analyses indicated that these gene families play fundamental roles in the adaptation of S. scabra to extreme environments. Additionally, phylogenomic analysis indicated a close evolutionary relationship between the genera Stylosanthes and Arachis. Finally, this study found a high number (57) of aquaporin-encoding loci in the S. scabra genome. RNA-Seq and qPCR data suggested that the PIP subfamily may play a key role in the species’ adaptation to water deficit conditions. Overall, these results provide valuable insights into S. scabra biology and a wealth of gene/transcript information for future legume omics studies.