Re-sequencing of Verticillium dahliae isolates reveals high genome plasticity

Verticillium spp. are soil-borne plant pathogens that are responsible for Verticillium wilt diseases on a wide range of host plants. They belong to the class of Deuteromycetes, a class of fungi for which no known sexual stage has been found. In our research we focus on V. dahliae, a plant pathogenic species within the Verticillium genus. In order to perform population genetics and comparative genomics, we have used massive parallel sequencing to determine the genome sequences of 11 V. dahliae isolates in addition to the publicly available genome of the V. dahliae isolate VdLs17. The isolates were selected based on whether they are pathogenic or not on Arabidopsis and tomato, and on aggressiveness. Sequences were assembled using a combination of mapping tools (SOAPaligner, Maq) and de novo assemblers (SOAPdenovo and Velvet). In our initial genome comparisons, whole genome mapping was performed to investigate structural differences on the scaffold level, and nucleotide diversity on the gene level, between the newly sequenced isolates and VdLs17. For most isolates, the largest percentage of reads (70-80%) could be mapped with high confidence and similarity to VdLs17. Furthermore, de novo assembly of the non-mappable reads and subsequent comparisons between isolates demonstrated high sequence diversification of some regions, as well as complete loss of other regions, demonstrating a high degree of plasticity of the V. dahliae genome