Comparative genomics reveals putative copper tolerance genes in a Fusarium oxysporum strain

Copper has been widely used as a main component in fungicides due to its versatility and effectivity. However, copper contamination from the environment creates selective pressure for the emergence of copper-tolerant pathogenic fungal strains that may proliferate and further cause damage to important agricultural crops. Although some studies focused on specific cellular mechanisms of copper tolerance, comprehensive genomic data are lacking. Here, we examined the genes potentially involved in copper tolerance by conducting a comparative analysis of newly sequenced genomes of 2 Fusarium oxysporum strains, IB-SN1W (copper-tolerant) and Foc-3429 (copper-sensitive), with other Fusarium species. Whole-genome assembly and annotation identified 10 core chromosomes shared between the 2 strains. Protein prediction revealed 16,894 and 15,420 protein-coding genes for IB-SN1W and Foc-3429, respectively. There are 388 unique genes in IB-SN1W not found in Foc-3429, potentially contributing to copper tolerance. Furthermore, the identification of synteny between the 2 strains, including the analysis of orthologous genes within the Fusarium genus, confirmed the presence of accessory chromosomes that are specific to IB-SN1W, accounting for 13% of the genome. These accessory chromosomes consist of genes associated with cation transporter activity, vacuole, copper oxidases, and copper transporters which shed light on the potential mechanism of copper tolerance in this strain. Additionally, a region within an accessory chromosome contains a high density of copper-related genes, raising the possibility that horizontal transfer of these chromosomes may contribute to copper tolerance.