Stylosanthes scabra, a legume native to the Brazilian semiarid region, exhibits remarkable drought tolerance and represents a valuable model for studying molecular adaptation in legumes. Transcription factors of the AP2/ERF superfamily play central roles in plant development and stress response. This study aimed to identify and characterize AP2/ERF genes in Stylosanthes scabra and to analyze their transcriptional response to root dehydration. Candidate genes were identified through a Hidden Markov Model (HMM) search using the AP2 domain profile (PF00847), followed by validation of conserved domains, physicochemical characterization, prediction of subcellular localization, phylogenetic and structural analyses, and functional annotation. A total of 295 AP2/ERF proteins were identified and designated as SscAP2/ERF, most of which were predicted to be localized in the nucleus. These proteins exhibited a wide range of molecular weights and isoelectric points, reflecting structural diversity, and were classified into four subfamilies: AP2, ERF, DREB, and RAV. Functional annotation revealed predominant roles in DNA binding and transcriptional regulation, while promoter analysis identified numerous stress-related cis-elements. A total of 32 transcripts were differentially expressed under 24 h of water deficit, and four selected genes had their expression patterns validated by qPCR. These findings provide new insights into the AP2/ERF gene subfamily in Stylosanthes scabra and lay the groundwork for future biotechnological approaches to enhance stress tolerance in legumes.

Plant viruses pose serious threats to global crop production, and members of the genus Tobamovirus are particularly problematic due to their environmental stability, efficient mechanical transmission and rapid global spread. Tomato brown rugose fruit virus (ToBRFV) has emerged as one of the most damaging tobamovirus affecting tomato, a crop of major economic importance worldwide. ToBRFV has been reported in more than 45 countries, including Portugal. However, to date, no peer-reviewed molecular characterization of local isolates has been published, and official records classify its presence in Portugal as transient. This study confirms the occurrence of ToBRFV and provides the first comprehensive genomic and phylogenetic characterization of local virus isolates in Portugal. RNA-seq generated 192,852,438 reads, of which 103,882,115 (58.9%) mapped to ToBRFV, allowing reconstruction of a complete 6393 nt viral genome. A second full-length consensus sequence was independently obtained from the same composite sample using an overlapping Sanger sequencing strategy, differing by only two SNPs. Comparative genomic, functional, structural, and phylogenetic analysis revealed low diversity, with most variation located in replicase-coding regions, while movement and coat protein genes remained highly conserved. Nucleotide-based phylogenies resolved geographically structured clades, although the Portuguese sequences formed a strongly supported subclade with a Chinese isolate. These findings support recent global dissemination of ToBRFV and reinforce the importance of integrated surveillance and genomic monitoring for effective virus management.

Transposable elements (TEs), which were once relegated to the status of genomic parasites, are today accepted as important agents of plant genome evolution and adaptation. This review integrates evidence pointing to their dual function as drivers of genetic diversity and instability, with a focus on their contribution to phenotypic innovation, stress tolerance, and crop trait control. TEs create structural and regulatory diversity by insertional mutagenesis, cis ‐regulatory sequence donation, and epigenetic interactions, facilitating fast adaptation to environmental stress. Advances in omics technologies have unraveled TE dynamics, showing insertion bias toward genic and regulatory regions and stress‐responsive activation patterns. The influence of the mobilome on crop improvement is emphasized by TE‐derived molecular markers, clustered regularly interspaced short palindromic repeats‐mediated TE regulation, and epigenome editing that minimizes risks of genome instability while tapping TE‐driven diversity. Rice ( Oryza sativa L.) mPing and maize ( Zea mays L.) Hopscotch , for instance, demonstrate TE potential in trait enhancement and domestication. Moreover, multi‐omics integration has defined TEs’ input into stress response and genome plasticity, offering new targets for precision breeding. Challenges remain in modeling TE behavior and weighing adaptive potential against harmful effects, requiring sophisticated computational models and synthetic biology strategies. Interdisciplinary approaches integrating machine learning and synthetic TE design should be prioritized in future research to maximize TE‐mediated crop resilience. With the integration of TE biology and cutting‐edge biotechnologies, global food security issues, fueled by climate change, can be mitigated by the scientific community. This overview situates TEs not merely as genomic leftovers but as essential next‐generation crop requirements, necessitating their strategic location in sustainable agro‐innovation.

Improper soil management for the development of important crops worldwide can jeopardize carbon (C) storage and soil organic matter (SOM) health. It was postulated that the application of vinasse to sugarcane soil under the control of agricultural machinery could increase C stocks and improve aggregate stability index, soil porosity and density, thus ensuring better root penetration. Therefore, in this study, the management system of sugarcane based on rainfed with vinasse application (RV), irrigated (I) and irrigated with vinasse application (IV) was studied in a tropical environment to determine the C stocks and the physical and chemical properties of the soil. The experimental design was randomized blocks with five replicates, and the organic C contents and stocks, soil density, total porosity, soil resistance to root penetration, and aggregate stability index (ASI) of sugarcane within rows and between rows were analyzed at 0–10- and 10–20- cm depth. The RV and IV treatments promoted the same potassium concentrations in the row and between the rows of sugarcane cultivation. The IV exhibited the highest soil ASI (74% at 0–10- and 77% at 10–20-cm depth) and stored approximately 70% more carbon than the I management. The use of sugarcane vinasse preserved the physical conditions of the soil, particularly in the inter-row area, by reducing surface layer compaction and increasing soil moisture and porosity, thereby representing a more sustainable long-term management system.