Abstract:In order to explore the reasons for the differences in OTA biosynthesis in different Aspergillus niger and remove and prevent toxins，Aspergillus niger CICC 41702 and Aspergillus niger 3.316 were selected as experimental materials. Whole-genome resequencing was used to analyze the genomic differences between the two Aspergillus niger strains and the mechanism of OTA biosynthesis. The whole-genome resequencing of the two Aspergillus niger strains producing and not producing OTA was performed by Illumina technology，and the genome sequence of Aspergillus niger CBS 513.88 was used as a reference.The information of single nucleotide polymorphism（SNP），insertions or deletions（InDel），structural variants（SV），copy number variation（CNV）was deeply mined，and specific bioinformatics analysis of genes involved in OTA biosynthesis was carried out. Aspergillus niger 3.316 showed higher variation than Aspergillus niger CICC 41702，and the An15g07920 gene had a large number of non-synonymous mutations in Aspergillus niger 3.316 and showed a deletion of 23 600 bp. It was speculated that this may be the reason for the difference in OTA biosynthesis between the two Aspergillus niger strains.