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.

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.