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Background  The genus  Microbotryum  includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease.  Microbotryum lychnidis-dioicae  infects  Silene latifolia  and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development.    Results  We determined the haploid genome sequence for  M. lychnidis-dioicae  and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions.    Conclusions  The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1660-8) contains supplementary material, which is available to authorized users.

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus