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Background  The cereal rust fungi are destructive pathogens that affect grain production worldwide. Although the genomic and transcript sequences for three  Puccinia  species that attack wheat have been released, the functions of large repertories of genes from  Puccinia  still need to be addressed to understand the infection process of these obligate parasites. Host-induced gene silencing (HIGS) has emerged a useful tool to examine the importance of rust fungus genes while growing within host plants. In this study, HIGS was used to test genes from  Puccinia  with transcripts enriched in haustoria for their ability to interfere with full development of the rust fungi.    Results  Approximately 1200 haustoria enriched genes from  Puccinia graminis  f. sp.  tritici  ( Pgt ) were identified by comparative RNA sequencing. Virus-induced gene silencing (VIGS) constructs with fragments of 86  Puccinia  genes, were tested for their ability to interfere with full development of these rust fungi. Most of the genes tested had no noticeable effects, but 10 reduced  Pgt  development after co-inoculation with the gene VIGS constructs and  Pgt . These included a predicted glycolytic enzyme, two other proteins that are probably secreted and involved in carbohydrate or sugar metabolism, a protein involved in thiazol biosynthesis, a protein involved in auxin biosynthesis, an amino acid permease, two hypothetical proteins with no conserved domains, a predicted small secreted protein and another protein predicted to be secreted with similarity to bacterial proteins involved in membrane transport. Transient silencing of four of these genes reduced development of  P. striiformis  ( Pst ) ,  and three of also caused reduction of  P. triticina  ( Pt ) development.    Conclusions  Partial suppression of transcripts involved in a large variety of biological processes in haustoria cells of  Puccinia  rusts can disrupt their development. Silencing of three genes resulted in suppression of all three rust diseases indicating that it may be possible to engineer durable resistance to multiple rust pathogens with a single gene in transgenic wheat plants for sustainable control of cereal rusts.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1791-y) contains supplementary material, which is available to authorized users.

Identification of promising host-induced silencing targets among genes preferentially transcribed in haustoria of Puccinia