Background: Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. However, little is known about the regulatory mechanism of tuber expansion. In order to identify the genes and miRNAs involved in tuber expansion, we examined the mRNAs and small RNAs in Dioscorea opposita (Chinese yam) cv. Guihuai 16 tuber during its initiation and expansion stages. Results: A total of 14,238 differentially expressed genes in yam tuber at its expansion stage were identified by using RNA sequencing technology. Among them, 5723 genes were up-regulated, and 8515 genes were down-regulated. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these differentially expressed genes are somehow involved in response to tuber expansion, including CDPK, CaM, CDL, SAUR, DELLA, SuSy, and expansin. In addition, 541 transcription factor genes showed differential expression during the expansion stage at transcriptional level. MADS, bHLH, and GRAS were involved in cell differentiation, division, and expansion, which may relate to tuber expansion. Noteworthy, data analysis revealed that 22 known tuber miRNAs belong to 10 miRNA families, and 50 novel miRNAs were identified. The integrated analysis of miRNA-mRNA showed that 4 known miRNAs and 11 genes formed 14 miRNA-target mRNA pairs were co-expressed in expansion stage. miRNA160, miRNA396, miRNA535 and miRNA5021 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage. Conclusion: The mRNA and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

Peanut faces yield constraints due to aluminum (Al) toxicity in acidic soils. The multidrug and toxic compound extrusion (MATE) family is known for extruding organic compounds and transporting plant hormones and secondary metabolites. However, the MATE transporter family has not yet been reported in peanuts under the Al stress condition. In this genome-wide study, we identified 111 genes encoding MATE proteins from the cultivated peanut genome via structural analysis, designated as AhMATE1–AhMATE111. Encoded proteins ranged from 258 to 582 aa residues. Based on their phylogenetic relationship and gene structure, they were classified into six distinct groups. Genes were distributed unevenly on twenty peanut chromosomes. Chr-05 exhibited the higher density of 12%, while chr-02 and chr-11 have the lowest 1% of these loci. Peanut MATE genes underwent a periodic strong to moderate purifying selection pressure during evolution, exhibiting both tandem and segmental duplication events. Segmental duplication accounted for 82% of the events, whereas tandem duplication represented 18%, with both events predominantly driving their moderate expansion. Further investigation of seven AhMATE genes expression profiles in peanut root tips resulted in distinct transcriptional responses at 4, 8, 12, and 24 h post-Al treatment. Notably, AhMATE genes exhibited greater transcriptional changes in the Al-tolerant cultivar 99-1507 compared to the Al-sensitive cultivar ZH2 (Zhonghua No.2). Our findings provide the first comprehensive genome-wide analysis of the MATE family in cultivated peanuts, highlighting their potential roles in response to Al stress.

This meta-analysis combined the results of 61 independent studies published in 2005–2025 to examine polyamine-mediated responses to aluminum, cadmium, lead, chromium, copper, manganese, and selenium stress in plants. The logarithm ratio of responses (lnRR) under the random-effects model was used to calculate the effect sizes. Polyamine application significantly (p < 0.001) enhanced plant growth, with strong increases in root elongation (lnRR = 0.490, 95% CI: 0.362–0.618), fresh weight (lnRR = 0.413, 95% CI: 0.347–0.480), and dry weight (lnRR = 0.475, 95% CI: 0.409–0.541). Oxidative stress was markedly reduced, as reflected by decreases in reactive oxygen species accumulation (lnRR = −0.585, 95% CI −0.682 to −0.487, p < 0.001), hydrogen peroxide content (lnRR = 0.005, 95% CI −0.244 to 0.254, p = 0.968), and lipid peroxidation (lnRR = −0.487, 95% CI −0.578 to −0.397, p < 0.001). The antioxidant defenses were strengthened, and the levels of superoxide dismutase (lnRR = 0.468, p < 0.001) and catalase activity (lnRR = 0.373, p < 0.001) increased significantly. Metal accumulation was consistently reduced in polyamine-treated plants (lnRR = −0.392, 95% CI −0.460 to −0.324, p < 0.001). Supplementary genetic-level data indicated that metal stress triggers polyamines to regulate metal transporters, polyamine biosynthesis genes, antioxidant-related genes, and hormone-signaling pathways. Collectively, these data points make polyamines a key controller of plant metal stress tolerance and offer a quantitative and mechanistic system to apply them to metal-impacted agroecosystems.

The circadian clock is an endogenous timekeeping system that coordinates plant growth, development, metabolism, and responses to environmental stimuli. Although circadian regulation has been implicated in multiple abiotic stress responses, its potential involvement in aluminum (Al) stress adaptation in peanut (Arachis hypogaea L.) remains poorly understood. A genome-wide analysis was performed to identify and characterize circadian clock genes in peanut and investigate their transcriptional responses to Al stress. A total of 74 circadian clock genes from Arabidopsis thaliana were used as reference sequences to identify homologous genes in the peanut genome. A total of 71 encoding circadian clock proteins were identified and comprehensively characterized through analyses of chromosomal distribution, conserved domains, motif composition, transmembrane regions, subcellular localization, phylogenetic relationships, functional annotation, and protein interaction networks. Transcriptome data (RNA-seq accession PRJNA525247) from Al-sensitive ZH2 (Zhonghua 2) and Al-tolerant 99-1507 peanut cultivars were further analyzed to evaluate gene expression patterns under Al stress. The identified genes were unevenly distributed across all 20 peanut chromosomes and exhibited diverse structural features and predicted biological functions. Phylogenetic analysis demonstrated a high degree of evolutionary conservation between peanut and Arabidopsis circadian clock genes. Functional annotation indicated that many identified genes are associated with transcriptional regulation, light perception, signal transduction, phytohormone signaling, and stress-responsive pathways. Comparative transcriptome analysis revealed distinct expression profiles between the Al-sensitive and Al-tolerant cultivars, with several genes, including homologs of XAP5, PIF3, GIGANTEA (GI), FLOWERING LOCUS T (FT), and AGL15, displaying cultivar-dependent responses to Al treatment, where these were upregulated in ZH2 but downregulated in 99-1507. These findings provide the first comprehensive overview of the circadian clock genes in peanut and suggest that circadian regulatory pathways may contribute to transcriptional responses associated with Al stress adaptation. This study establishes a valuable genomic resource for future functional characterization of circadian clock genes and supports molecular breeding efforts for rhythmic traits for Al tolerance in cultivated peanuts.