Transcriptome-Based WGCNA Analysis Reveals the Mechanism of Drought Resistance Differences in Sweetpotato (Ipomoea batatas (L.) Lam.)

Integration WGCNA with LC-MS data for evaluating the processing status and transformation rules of Ligustri Lucidi Fructus: A novel strategy for evaluating the processing technology of traditional Chinese medicines

Ligustri Lucidi Fructus (LLF) is a traditional Chinese medicine (TCM) to treat hepatopathy and osteopathy. Wine-processed LLF (WLLF) was much more widely used than raw LLF (RLLF) in clinical practice, however, there is no consensus on processing time. To investigate the processing status of WLLF and transformation rules during processing, a UHPLC-Q-Orbitrap-MS method combined with data-independent acquisition (DIA) mode was firstly established and 227 compounds were identified or tentatively identified. Subsequently, a novel strategy using integration weighted gene co-expression network analysis (WGCNA) with LC-MS data was proposed. A total of 73 differential metabolites were screened out between RLLF and WLLF (wine steaming for 18 h). Meanwhile, the concentration of 11 differential compounds for WLLF was quantified. Finally, correlations between compounds were analyzed by WGCNA and the top five compounds negatively correlated with salidroside were validated, revealing that G13, specnuezhenide, oleuropein, acteoside, and neonuzhenide could be transformed into salidroside and its analogues during processing, respectively. The results indicated that our proposed strategy could be effectively employed to evaluate the processing status of TCMs.

Multi-omics analysis of Streptomyces djakartensis strain MEPS155 reveal a molecular response strategy combating Ceratocystis fimbriata causing sweet potato black rot

To investigate the potential antifungal mechanisms of rhizosphere Actinobacteria against Ceratocystis fimbriata in sweet potato, a comprehensive approach combining biochemical analyses and multi-omics techniques was employed in this study. A total of 163 bacterial strains were isolated from the rhizosphere soil of sweet potato. Among them, strain MEPS155, identified as Streptomyces djakartensis, exhibited robust and consistent inhibition of C. fimbriata mycelial growth in in vitro dual culture assays, attributed to both cell-free supernatant and volatile organic compounds. Moreover, strain MEPS155 demonstrated diverse plant growth-promoting attributes, including the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, phosphorus solubilization, nitrogen fixation, and enzymatic activities such as cellulase, chitinase, and protease. Notably, strain MEPS155 exhibited efficacy against various sweet potato pathogenic fungi. Following the inoculation of strain MEPS155, a significant reduction (P < 0.05) in malondialdehyde content was observed in sweet potato slices, indicating a potential protective effect. The whole genome of MEPS155 was characterized by a size of 8,030,375 bp, encompassing 7234 coding DNA sequences and 32 secondary metabolite biosynthetic gene clusters. Transcriptomic analysis revealed 1869 differentially expressed genes in the treated group that cultured with C. fimbriata, notably influencing pathways associated with porphyrin metabolism, fatty acid biosynthesis, and biosynthesis of type II polyketide products. These alterations in gene expression are hypothesized to be linked to the production of secondary metabolites contributing to the inhibition of C. fimbriata. Metabolomic analysis identified 1469 potential differently accumulated metabolites (PDAMs) when comparing MEPS155 and the control group. The up-regulated PDAMs were predominantly associated with the biosynthesis of various secondary metabolites, including vanillin, myristic acid, and protocatechuic acid, suggesting potential inhibitory effects on plant pathogenic fungi. Our study underscores the ability of strain S. djakartensis MEPS155 to inhibit C. fimbriata growth through the production of secretory enzymes or secondary metabolites. The findings contribute to a theoretical foundation for future investigations into the role of MEPS155 in postharvest black rot prevention in sweet potato.

Identification and core gene-mining of Weighted Gene Co-expression Network Analysis-based co-expression modules related to flood resistance in quinoa seedlings

BACKGROUND

As an emerging food crop with high nutritional value, quinoa has been favored by consumers in recent years; however, flooding, as an abiotic stress, seriously affects its growth and development. Currently, reports on the molecular mechanisms related to quinoa waterlogging stress responses are lacking; accordingly, the core genes related to these processes were explored via Weighted Gene Co-expression Network Analysis (WGCNA).

RESULTS

Based on the transcriptome data, WGCNA was used to construct a co-expression network of weighted genes associated with flooding resistance-associated physiological traits and metabolites. Here, 16 closely related co-expression modules were obtained, and 10 core genes with the highest association with the target traits were mined from the two modules. Functional annotations revealed the biological processes and metabolic pathways involved in waterlogging stress, and four candidates related to flooding resistance, specifically AP2/ERF, MYB, bHLH, and WRKY-family TFs, were also identified.

CONCLUSIONS

These results provide clues to the identification of core genes for quinoa underlying quinoa waterlogging stress responses. This could ultimately provide a theoretical foundation for breeding new quinoa varieties with flooding tolerance.

The APSES transcription factor CfSwi6 is required for growth, cell wall integrity, and pathogenicity of Ceratocystis fimbriata

Cell wall integrity (CWI) is crucial for the growth, development, and host invasion of pathogenic fungi. The APSES transcription factor Swi6 in fungi plays a role in mediating cell wall integrity through the mitogen-activated protein kinase (MAPK) signaling pathway. Ceratocystis fimbriata is a notorious pathogenic fungus responsible for causing black rot in sweet potatoes. In this study, an orthologous APSES transcription factor Swi6 (CfSwi6) downstream of the CWI regulatory pathway in C. fimbriata was characterized. Deletion of CfSWI6 leads to impaired hyphal development, conidiation, and compromised cell wall integrity, resulting in a significant reduction in virulence. Transcriptome analysis revealed the involvement of CfSWI6 in various pathways, including the MAPK pathway, DNA synthesis and stress response. ChIP-seq data provided predictions of potential target genes regulated by CfSwi6. Through yeast one-hybrid, we confirmed the direct binding of CfSwi6 to the promoter of the chitin synthetase gene. In summary, these findings indicated that CfSwi6 plays an important role in the growth, development, and pathogenicity of C. fimbriata. This study provides new insights into the pathogenic mechanism of C. fimbriata in sweet potato and inspires potential strategies to control sweet potato black rot.