Xyloglucan endotransglucosylases/hydrolases (XTHs) are key enzymes involved in cell wall remodeling that play roles in plant responses to environmental stress. Despite their importance, a comprehensive investigation of the XTH gene family in cassava (Manihot esculenta Crantz), a crucial drought-tolerant crop in tropical and subtropical regions, has not yet been conducted. In the present study, we identified 37 XTH genes (MeXTH1-37) within the cassava genome, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). Phylogenetic analysis grouped 37 MeXTH genes into three distinct clades, a classification further supported by exon–intron organizations and the conserved protein motif architectures. Duplication events, particularly segmental duplication, were identified as the main driving force for MeXTH gene expansion in cassava. Comparative synteny analysis revealed orthologous relationships between MeXTH genes and XTH-related genes in seven other plant species, including soybean, poplar, tomato, Arabidopsis, maize, wheat, and rice. Global expression analysis revealed that MeXTH genes display different expression patterns in various cassava tissues, shedding light on their potential biological functions. Furthermore, quantitative real-time PCR (qRT-PCR) analysis of 12 representative MeXTH genes under salt and osmotic stress, as well as salicylic acid (SA) and methyl jasmonate (MeJA) treatments, demonstrated their differential responses to these stimuli. These results provide novel insights into the role of the MeXTH gene family in enhancing cassava’s tolerance to abiotic stress.

Dirigent (DIR) genes play a pivotal role in plant development and stress adaptation. Manihot esculenta Crantz, commonly known as cassava, is a drought-resistant plant thriving in tropical and subtropical areas. It is extensively utilized for starch production, bioethanol, and animal feed. However, a comprehensive analysis of the DIR family genes remains unexplored in cassava, a crucial cash and forage crop in tropical and subtropical regions. In this study, we characterize a total of 26 cassava DIRs (MeDIRs) within the cassava genome, revealing their uneven distribution across 13 of the 18 chromosomes. Phylogenetic analysis classified these genes into four subfamilies: DIR-a, DIR-b/d, DIR-c, and DIR-e. Comparative synteny analysis with cassava and seven other plant species (Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum)) provided insights into their likely evolution. We also predict protein interaction networks and identify cis-acting elements, elucidating the functional differences in MeDIR genes. Notably, MeDIR genes exhibited specific expression patterns across different tissues and in response to various abiotic and biotic stressors, such as pathogenic bacteria, cadmium chloride (CdCl₂), and atrazine. Further validation through quantitative real-time PCR (qRT-PCR) confirmed the response of DIR genes to osmotic and salt stress. These findings offer a comprehensive resource for understanding the characteristics and biological functions of MeDIR genes in cassava, enhancing our knowledge of plant stress adaptation mechanisms.

Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root responses to P. indica colonization at 10 days after inoculation (dais; early stage) and 20 dais (late stage) during symbiosis establishment. Colonization was confirmed by phenotypic and physiological assessments, with inoculated plants showing enhanced root growth; colonized roots exhibited higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), along with increased indole-3-acetic acid (IAA) levels, whereas malondialdehyde (MDA), jasmonic acid (JA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were reduced. Transcriptome and metabolomic profiling identified 1884 and 1077 differentially expressed genes (DEGs) and 2098 and 1509 differentially accumulated metabolites (DAMs) at 10 dais (Pi10d vs. CK10d) and 20 dais (Pi20d vs. CK20d), respectively, and 3355 DEGs and 2314 DAMs between stages (Pi20d vs. Pi10d). Functional enrichment highlighted key pathways related to secondary metabolism, carbohydrate metabolism, and lipid biosynthesis. Differentially expressed transcription factors spanned multiple families, including MYB, AP2/ERF, MADS-box, and bZIP, consistent with broad transcriptional reprogramming during symbiosis establishment. Integrative multi-omics analysis further highlighted phenylpropanoid biosynthesis and α-linolenic acid metabolism as consistently co-enriched pathways, suggesting coordinated shifts in gene expression and metabolite accumulation across colonization stages. Collectively, these results provide a multi-layered resource and a framework for mechanistic dissection of the P. indica–B. decumbens interaction.