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Background   Magnaporthe oryzae  (anamorph  Pyricularia oryzae ) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of  M. oryzae , we carried out whole genome resequencing of four  M. oryzae  isolates from rice ( Oryza sativa) , one from foxtail millet ( Setaria italica ), three from wild foxtail millet  S. viridis,  and one isolate each from finger millet ( Eleusine coracana) , wheat ( Triticum aestivum)  and oat ( Avena sativa) , in addition to an isolate of a sister species  M. grisea , that infects the wild grass  Digitaria sanguinalis .    Results  Whole genome sequence comparison confirmed that  M. oryzae Oryza  and  Setaria  isolates form a monophyletic and close to another monophyletic group consisting of isolates from  Triticum  and  Avena . This supports previous phylogenetic analysis based on a small number of genes and molecular markers. When comparing the host specific subgroups, 1.2–3.5 % of genes showed presence/absence polymorphisms and 0–6.5 % showed an excess of non-synonymous substitutions. Most of these genes encoded proteins whose functional domains are present in multiple copies in each genome. Therefore, the deleterious effects of these mutations could potentially be compensated by functional redundancy. Unlike the accumulation of nonsynonymous nucleotide substitutions, gene loss appeared to be independent of divergence time. Interestingly, the loss and gain of genes in pathogens from the  Oryza  and  Setaria  infecting lineages occurred more frequently when compared to those infecting  Triticum  and  Avena  even though the genetic distance between  Oryza  and  Setaria  lineages was smaller than that between  Triticum  and  Avena  lineages. In addition, genes showing gain/loss and nucleotide polymorphisms are linked to transposable elements highlighting the relationship between genome position and gene evolution in this pathogen species.    Conclusion  Our comparative genomics analyses of host-specific  M. oryzae  isolates revealed gain and loss of genes as a major evolutionary mechanism driving specialization to  Oryza  and  Setaria . Transposable elements appear to facilitate gene evolution possibly by enhancing chromosomal rearrangements and other forms of genetic variation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2690-6) contains supplementary material, which is available to authorized users.

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements