Comparative analysis towards the identification of genome wide characteristics of a beneficial fungal endophyte-Genome assembly

illumina/Nanopore reads for genome assembly of FsK S3,S9: Biological replicates for FsK paired end illumina data combined_ont_pass.fastq.gz: reads that passed the quality threshold of the nanopore sequencer hc: highest gzip compression level(9) Fusarium solani strain K (FsK) is an endophytic fungus with a wide host range that protects its host plants against pathogens and environmental stresses. In this study, we performed de novo genome sequencing and annotation, while a phylogenomic analysis confirmed the placement of FsK within the Fusarium solani species complex (FSSC). A comprehensive comparative genomics analysis was conducted with species that can colonize tomato as a common host, namely the beneficial basidiomycete Serendipita indica and the arbuscular mycorrhizal fungus Rhizophagus irregularis, both model symbiotic organisms in their respective fungal divisions, as well as the closely pathogenic Fusarium vanettenii 77-13-4. To identify mechanisms of early-stage FsK-plant interaction and fungal adaptation, comparative analysis of secreted effectors, carbohydrate-active enzymes and secondary metabolite clusters, was performed. FsK specific genes implicated in DNA repair and iron acquisition via ferrirhodin synthesis, highlighting adaptation to stress conditions and possible mutualistic functions with plant hosts were identified. These findings provide valuable insights into the genomic determinants of fungal lifestyles within the FSSC and establish a foundation for future functional studies on fungal-plant interactions in agricultural contexts.用于FsK基因组组装的Illumina测序读段与Nanopore测序读段 S3、S9：FsK双端Illumina测序数据的生物学重复样本 combined_ont_pass.fastq.gz：通过Nanopore测序仪质量阈值的测序读段 hc：最高级gzip压缩（压缩等级为9） 茄病镰刀菌K菌株（Fusarium solani strain K, FsK）是一种宿主范围广泛的内生真菌，可保护其宿主植物抵御病原菌侵染与环境胁迫。本研究完成了FsK的从头基因组测序与注释，同时通过系统基因组学分析确认了FsK在茄病镰刀菌物种复合体（Fusarium solani species complex, FSSC）中的分类地位。 本研究以可共同定殖番茄的物种作为参照开展全面比较基因组学分析，包括有益担子菌印度梨形孢（Serendipita indica）、丛枝菌根真菌不规则根囊霉（Rhizophagus irregularis）——二者分别是各自真菌门类中的模式共生生物——以及亲缘关系紧密的致病菌株凡内特镰刀菌77-13-4（Fusarium vanettenii 77-13-4）。 为解析FsK与植物早期互作及真菌适应性的分子机制，本研究对分泌效应蛋白、碳水化合物活性酶及次级代谢产物基因簇开展了比较分析。研究鉴定出FsK特有的参与DNA修复以及通过铁杆菌素合成途径获取铁离子的基因，这些基因揭示了FsK对胁迫环境的适应性，以及其与植物宿主间可能存在的共生功能。 上述研究结果为解析FSSC内真菌生活方式的基因组决定因素提供了重要参考，同时为农业场景下真菌-植物互作的后续功能研究奠定了坚实基础。