Heterobasidion annosum (Fr.) Bref. sensu lato (s.l.) is a necrotrophic pathogen causing damage to conifers in the Northern Hemisphere. H. annosum s.l. consists of five species: three European [H. annosum sensu stricto (s.s.), H. parviporum and H. abietinum] and two North American (H. irregulare and H. occidentale); all with different but partially overlapping host preferences. A multilocus phylogenetic tree was built and the divergence times were estimated. Plate tectonics is likely to have been the main factor influencing Heterobasidion speciation and biogeography. Along with the geographical separation, the Heterobasidion species have specialized on different host genera. The H. annosum species complex originated in Laurasia and the H. annosum s.s./H. irregulare and H. parviporum/H. abietinum/H. occidentale ancestral species emerged between 45 million–60 million years ago in the Palaearctic. The data imply that H. irregulare and H. occidentale colonized North America via different routes: H. irregulare colonizing from the east via Trans Atlantic land bridges and H. occidentale colonizing from the west via the Bering Land Bridge. Alternatively H. occidentale originated from North America. Identification of virulence factors is important for understanding the Heterobasidion–conifer pathosystem. Two studies of genetic mapping of virulence were performed. Virulence traits were measured as lesion length in the phloem and fungal growth in the sapwood of pine and spruce. Quantitative trait loci (QTL) were identified and positioned on a genetic linkage map for virulence of 102 progeny isolates from a cross between H. irregulare and H. occidentale. Both virulence traits in Picea abies identified significant QTLs on linkage group (LG) 15. Another QTL was positioned on LG 15 for the lesion length measurement in Pinus sylvestris. Moreover, QTLs on two separate smaller LGs were identified for fungal growth in sapwood and lesion length, respectively. The QTLs probably represent loci important for specific as well as general aspects of virulence on P. sylvestris and P. abies. A genome-wide association study was performed for virulence on 23 H. annosum s.s. isolates. Twelve SNP markers distributed on seven contigs were significantly associated with virulence. From these, three regions were characterized, two with one marker each with the lowest p-values and one region containing six markers. The linkage disequilibrium blocks in these regions ranged between 1.2 and 31.2 kb. Seven genes were identified as candidate virulence determinants encoding calcineurin, acetylglutamate kinase/synthase, cytochrome P450 monooxygenase, serine carboxypeptidase, quinone oxidoreductase (ToxD) and two flavin-containing monooxygenases
