Genome analyses reveal the secondary metabolites potentially influence the geographical distribution ofFusarium pseudograminearumpopulations

Abstract

AbstractFusarium crown rot (FCR), caused byFusarium pseudograminearum, significantly impacts wheat yield and quality in China’s Huanghuai region. The rapidF. pseudograminearumepidemic and FCR outbreak within a decade remain unexplained. In this study, two high-quality, chromosome-level genomes ofF. pseudograminearumstrains 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) amongF. pseudograminearumstrains were analyzed. The whole-genome SNP locus based population classification mirrored the toxin chenotype (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 (SMGC) loci were located in SNP-dense genomic regions, suggesting high mutability and a possible contribution toF. pseudograminearumpopulation structure and environmental adaptability. This study provides insightful perspectives on the distribution and evolution ofF. pseudograminearum, and for forecasting the spread of wheat FCR, thereby aiding in the development of preventive measures and control strategies.