Abstract：
Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, significantly impacts wheat yield and quality in China\'s Huanghuai region. The rapid F. pseudograminearum epidemic and FCR outbreak within a decade remain unexplained. In this study, two high-quality, chromosome-level genomes of F. pseudograminearum strains producing 3-acetyl-deoxynivalenol (3AcDON) and 15-acetyl-deoxynivalenol (15AcDON) toxins were assembled. Additionally, 38 related strains were resequenced. Genomic differences such as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations (SVs) among F. pseudograminearum strains were analyzed. The whole-genome SNP locus-based population classification mirrored the toxin chemotype (3AcDON and 15AcDON)-based classification, indicating the presence of genes associated with the trichothecene toxin gene cluster. Further analysis of differential SNP, indel, and SV loci between the 3AcDON and 15AcDON populations revealed a predominant connection to secondary metabolite synthesis genes. Notably, the majority of the secondary metabolite biosynthesis gene cluster loci were located in SNP-dense genomic regions, suggesting high mutability and a possible contribution to F. pseudograminearum population structure and environmental adaptability. This study provides insightful perspectives on the distribution and evolution of F. pseudograminearum and for forecasting the spread of wheat FCR, thereby aiding in the development of preventive measures and control strategies.
摘要：
镰刀菌冠腐病(FCR),由假镰刀菌引起的，黄淮地区小麦产量和品质的显著影响。十年内迅速发生的假赤霉病流行和FCR爆发仍无法解释。在这项研究中,两个高质量的，组装了产生3-乙酰基-脱氧雪腐镰刀菌烯醇（3AcDON）和15-乙酰基-脱氧雪腐镰刀菌烯醇（15AcDON）毒素的假赤霉病菌菌株的染色体水平基因组。此外,对38株相关菌株进行重测序。基因组差异，如单核苷酸多态性（SNP），插入/删除(indel)，并分析了假赤霉病菌株之间的结构变异（SV）。基于全基因组SNP基因座的群体分类反映了基于毒素化学型（3AcDON和15AcDON）的分类，表明存在与单端孢菌毒素基因簇相关的基因。进一步分析差异SNP，indel,3AcDON和15AcDON种群之间的SV基因座显示出与次生代谢物合成基因的主要联系。值得注意的是,大多数次级代谢产物生物合成基因簇（SMGC）基因座位于SNP密集的基因组区域，表明高度的突变性和对假草的种群结构和环境适应性的可能贡献。本研究为假赤霉的分布和进化提供了有见地的观点，为了预测小麦FCR的传播，从而帮助制定预防措施和控制策略。
