Background Ammonium transporters (AMTs), a family of proteins transporting ammonium salt and its analogues, have been studied in many aspects. Although numerous studies have found that ammonium affects the interaction between plants and pathogens, the role of AMTs remains largely unknown, especially that of the AMT2-type AMTs. Results In the present study, we found that the concentration of ammonium in wheat leaves decreased after infection with Puccinia striiformis f. sp . tritici ( Pst ), the causal agent of stripe rust. Then, an AMT2-type ammonium transporter gene induced by Pst was identified and designated as TaAMT2;3a . Transient expression assays indicated that TaAMT2;3a was located to the cell and nuclear membranes. TaAMT2;3a successfully complemented the function of a yeast mutant defective in NH 4 + transport, indicating its ammonium transport capacity. Function of TaAMT2;3a in wheat- Pst interaction was further analyzed by barley stripe mosaic virus (BSMV)-induced gene silencing. Pst growth was significantly retarded in TaAMT2;3a -knockdown plants, in which ammonium in leaves were shown to be induced at the early stage of infection. Histological observation showed that the hyphal length, the number of hyphal branches and haustorial mother cells decreased in the TaAMT2;3a knockdown plants, leading to the impeded growth of rust pathogens. Conclusions The results clearly indicate that the induction of AMT2-type ammonium transporter gene TaAMT2;3a may facilitates the nitrogen uptake from wheat leaves by Pst, thereby contribute to the infection of rust fungi. Electronic supplementary material The online version of this article (10.1186/s12870-019-1841-8) contains supplementary material, which is available to authorized users.

Puccinia striiformis f. sp. tritici (Pst) is the causal agent of wheat stripe rust that causes severe yield losses all over the world. As a macrocyclic heteroecious rust fungus, it is able to infect two unrelated host plants: wheat and barberry. Its urediniospores infect wheat and cause disease epidemic, while its basidiospores parasitize barberry to fulfill the sexual reproduction. This complex life cycle poses interesting questions on the different mechanisms of pathogenesis underlying the infection of the two different hosts. In the present study, transcriptomes of Pst during the initial infection of wheat and barberry leaves were qualitatively and quantitatively compared. As a result, 142 wheat-specific expressed genes (WEGs) were identified, which was far less than 2,677 barberry-specifically expressed genes (BEGs). A larger proportion of evolutionary conserved genes were observed in BEGs than that in WEGs, implying a longer history of the interaction between Pst and barberry. Additionally, Pst differentially expressed genes (DEGs) between wheat at 1 dpi/2 dpi and barberry at 3 dpi/ 4dpi were identified by quantitative analysis. Gene Ontology analysis of these DEGs and expression patterns of Pst pathogenic genes, including those encoding candidate secreted effectors, cell wall degrading enzymes, and nutrient transporters, demonstrated that urediniospores and basidiospores exploited distinct strategies to overcome host defense systems. These results represent the first analysis of the Pst transcriptome in barberry and contribute to a better understanding of the evolutionary processes and strategies of different types of rust spores during the infection process on different hosts.