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.

中文翻译：

---

利用基因组和转录组学分析揭示解淀粉芽孢杆菌菌株 GKT04 抗枯萎病的抗真菌机制

内生细菌，特别是芽孢杆菌属成员的应用，由于其可持续性和生态安全性，为植物真菌病害的生物防治提供了一种有前景的策略。尽管已在多种内生细菌中鉴定出多种具有抗真菌能力的次级代谢物，但其生物合成的调节机制仍然很大程度上未知。为了阐明这一点，我们对解淀粉芽孢杆菌GKT04的整个基因组进行了测序，这是一种从香蕉根中分离出来的菌株，它对尖孢镰刀菌具有很高的抑制活性F。sp。立方比赛 4 (FOC4)。GKT04基因组由一个环状染色体和一个环状质粒组成，其中包含4,087个蛋白质编码基因和113个RNA基因。确定了八个可能编码抗真菌成分的基因簇。我们进一步应用 RNA-Seq 分析来调查 GKT04 菌株在 FOC4 抑制过程中基因表达的全基因组变化。总共鉴定了 575 个上调和 242 个下调基因，这些基因富含几种氨基酸和碳水化合物代谢途径。具体而言，与艰难梭菌素、杆菌肽和杆菌肽相关的基因簇显着上调，并构建了它们的基因调控网络。因此，我们的工作提供了对该B的基因组特征和基因表达模式的见解。amyloliquefaciens菌株，为枯萎病的生物防治提供了极好的潜力。