The application of endophytic bacteria, particularly members of the genus Bacillus, offers a promising strategy for the biocontrol of plant fungal diseases, owing to their sustainability and ecological safety. Although multiple secondary metabolites that demonstrate antifungal capacity have been identified in diverse endophytic bacteria, the regulatory mechanisms of their biosynthesis remain largely unknown. To elucidate this, we sequenced the entire genome of Bacillus amyloliquefaciens GKT04, a strain isolated from banana root, which showed high inhibitory activity against Fusarium oxysporum f. sp. cubense race 4 (FOC4). The GKT04 genome consists of a circular chromosome and a circular plasmid, which harbors 4,087 protein‐coding genes and 113 RNA genes. Eight gene clusters that could potentially encode antifungal components were identified. We further applied RNA‐Seq analysis to survey genome‐wide changes in the gene expression of strain GKT04 during its inhibition of FOC4. In total, 575 upregulated and 242 downregulated genes enriched in several amino acid and carbohydrate metabolism pathways were identified. Specifically, gene clusters associated with difficidin, bacillibactin, and bacilysin were significantly upregulated, and their gene regulatory networks were constructed. Our work thereby provides insights into the genomic features and gene expression patterns of this B. amyloliquefaciens strain, which presents an excellent potential for the biocontrol of Fusarium wilt.

Lepidopteran borers stand out as the most destructive pests in sugarcane, leading to reductions in stalk weight, juice quality and sugar recovery. Presently, integrated pest management (IPM) systems are utilized for sugarcane borer management, employing diverse methods encompassing cropping system, chemical pesticides, behavioral manipulation, biological agents and the selection of resistant varieties. However, the effectiveness of this strategy remains controversial due to concerns about harmful residues, formulation limitations, environmental variability, labor shortages and increased input costs. Currently, multiple lines of transgenic sugarcane expressing insecticidal genes from the bacterium Bacillus thuringiensis (Bt) have been developed globally, offering the prospect of increases production with reduced pesticides application, thereby eliminating the negative effect of IPM. In Brazil, the first genetically modified sugarcane cultivars resistant to the sugarcane borer have been approved and released for commercial cultivation, shedding a bright light on a viable solution for sugarcane borers. This paper reviews borer species and distribution, the significant damage caused by sugarcane borers, current control approaches and the future effective control strategies. Additionally, this work provides comprehensive understanding on Bt sugarcane, serving as an additional tool to complement conventional sugarcane borers control resistance programs.

Background: Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense race 4 (Foc4), is the most lethal disease of bananas in Asia. Methods: To better understand the defense response of banana to Fusarium wilt, the transcriptome and metabolome profiles of the roots from resistant and susceptible bananas inoculated with Foc4 were compared. Results: After Foc4 inoculation, there were 172 and 1,856 differentially expressed genes (DEGs) in the Foc4-susceptible variety (G1) and Foc4-resistant variety (G9), respectively. In addition, a total of 800 DEGs were identified between G1 and G9, which were mainly involved in the oxidation-reduction process, cell wall organization, phenylpropanoid biosynthesis, and lipid and nitrogen metabolism, especially the DEGs of Macma4_08_g22610, Macma4_11_g19760, and Macma4_03_g06480, encoding non-classical arabinogalactan protein; GDSL-like lipase; and peroxidase. In our study, G9 showed a stronger and earlier response to Foc4 than G1. As the results of metabolomics, lipids, phenylpropanoids and polyketides, organic acids, and derivatives played an important function in response to Fusarium wilt. More importantly, Macma4_11_g19760 might be one of the key genes that gave G9 more resistance to Foc4 by a lowered expression and negative regulation of lipid metabolism. This study illustrated the difference between the transcriptomic and metabolomic profiles of resistant and susceptible bananas. These results improved the current understanding of host-pathogen interactions and will contribute to the breeding of resistant banana plants.

Background: Lodging seriously affects sugarcane stem growth and sugar accumulation, reduces sugarcane yield and sucrose content, and impedes mechanization. However, the molecular mechanisms underlying sugarcane lodging tolerance remain unclear. In this study, comprehensive transcriptomic and proteomic analyses were performed to explore the differential genetic regulatory mechanisms between upright (GT42) and lodged (GF98-296) sugarcane varieties. Results: The stain test showed that GT42 had more lignin and vascular bundles in the stem than GF98-296. The gene expression analysis revealed that the genes that were differentially expressed between the two varieties were mainly involved in the phenylpropanoid pathway at the growth stage. The protein expression analysis indicated that the proteins that were differentially expressed between the two varieties were related to the synthesis of secondary metabolites, the process of endocytosis, and the formation of aminoacyl-tRNA. Time-series analysis revealed variations in differential gene expression patterns between the two varieties, whereas significant protein expression trends in the two varieties were largely consistent, except for one profile. The expression of CYP84A, 4CL, and CAD from the key phenylpropanoid biosynthetic pathway was enhanced in GT42 at stage 2 but suppressed in GF98-296 at the growth stage. Furthermore, the expression of SDT1 in the nicotinate and nicotinamide metabolism was enhanced in GT42 cells but suppressed in GF98-296 cells at the growth stage. Conclusion: Our findings provide reference data for mining lodging tolerance-related genes that are expected to facilitate the selective breeding of sugarcane varieties with excellent lodging tolerance.

Mango is a tropical fruit with high economic value. The selection of suitable dwarf mango varieties is an important aspect of mango breeding. However, the mechanisms that regulate mango dwarfing remain unclear. In this study, we compared the transcriptomes and metabolomes of mango varieties Guiqi (a dwarfed variety) and Jinhuang (an arborized variety). A total of 4,954 differentially expressed genes and 317 differentially abundant metabolites were identified between the two varieties, revealing the molecular mechanism of the gibberellin 3β-hydroxylase gene GA3ox in regulating dwarfing traits in mangoes using joint transcriptome and metabolome analyses. The results showed that differentially expressed genes were enriched in the diterpenoid biosynthesis pathway and that differentially abundant metabolites were annotated to their upstream pathway, the terpenoid backbone biosynthesis. A gene regulation network based on these two pathways was constructed, indicating the upregulation of the GA3ox gene and the accumulation of gibberellin in dwarfed mangoes. We then transferred the GA3ox gene to tobacco plants following the application of gibberellin, and the morphology and height of the transgenic tobacco plants largely recovered the phenotype. These results demonstrated that GA3ox plays a role in the regulation of dwarf traits. Our study provides an important theoretical basis for studying the regulatory mechanisms underlying mango dwarfism to facilitate mango breeding.