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Background  Downy mildew, caused by the oomycete pathogen  Sclerospora graminicola , is an economically important disease of Gramineae crops including foxtail millet ( Setaria italica ). Plants infected with  S. graminicola  are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches’ broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of  S. graminicola .    Results  Sequence reads were generated from  S. graminicola  using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in  S. graminicola  compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the  S. graminicola  lifecycle.    Conclusions  We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of  in planta -induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4296-z) contains supplementary material, which is available to authorized users.

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews