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Background   Brassica  plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by  Verticillium longisporum  is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2  V. longisporum  field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed.    Results  The draft genomes of 2  Verticillium longisporum  single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70 Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in  V. dahliae  and  V. albo-atrum . Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the  V. longisporum  genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to  V. dahliae . Presence of the mating-type genes  MAT1–1-1  and  MAT1–2-1  in the  V. longisporum  genomes were confirmed. However, the  MAT  genes in  V. dahliae, V. albo-atrum  and  V. longisporum  have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species.    Conclusions  The established draft genome of  V. longisporum  is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two  V. longisporum  genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to  V. dahliae . Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.    Electronic supplementary material  The online version of this article (doi: 10.1186/s12864-017-4407-x) contains supplementary material, which is available to authorized users.

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum