BackgroundRust fungi constitute the largest group of plant fungal pathogens. However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of inhibitory compounds and prevents their analysis from an evolutionary perspective. Gymnosporangium yamadae and G. asiaticum are two closely related rust fungal species, which are ecologically and economically important pathogens that cause apple rust and pear rust, respectively, proved to be devastating to orchards. In this study, we investigated the transcriptomes of these two Gymnosporangium species during the telial stage of their lifecycles. The aim of this study was to understand the evolutionary patterns of these two related fungi and to identify genes that developed by selection.ResultsThe transcriptomes of G. yamadae and G. asiaticum were generated from a mixture of RNA from three biological replicates of each species. We obtained 49,318 and 54,742 transcripts, with N50 values of 1957 and 1664, for G. yamadae and G. asiaticum, respectively. We also identified a repertoire of candidate effectors and other gene families associated with pathogenicity. A total of 4947 pairs of putative orthologues between the two species were identified. Estimation of the non-synonymous/synonymous substitution rate ratios for these orthologues identified 116 pairs with Ka/Ks values greater than1 that are under positive selection and 170 pairs with Ka/Ks values of 1 that are under neutral selection, whereas the remaining 4661 genes are subjected to purifying selection. We estimate that the divergence time between the two species is approximately 5.2 Mya.ConclusionThis study constitutes a de novo assembly and comparative analysis between the transcriptomes of the two rust species G. yamadae and G. asiaticum. The results identified several orthologous genes, and many expressed genes were identified by annotation. Our analysis of Ka/Ks ratios identified orthologous genes subjected to positive or purifying selection. An evolutionary analysis of these two species provided a relatively precise divergence time. Overall, the information obtained in this study increases the genetic resources available for research on the genetic diversity of the Gymnosporangium genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4059-x) contains supplementary material, which is available to authorized users.

Apple rust disease caused by Gymnosporangium yamadae is one of the major threats to apple orchards. In this study, dual RNA-seq analysis was conducted to simultaneously monitor gene expression profiles of G. yamadae and infected apple leaves during the formation of rust spermogonia and aecia. The molecular mechanisms underlying this compatible interaction at 10 and 30 days postinoculation (dpi) indicate a significant reaction from the host plant and comprise detoxication pathways at the earliest stage and the induction of secondary metabolism pathways at 30 dpi. Such host reactions have been previously reported in other rust pathosystems and may represent a general reaction to rust infection. G. yamadae transcript profiling indicates a conserved genetic program in spermogonia and aecia that is shared with other rust fungi, whereas secretome prediction reveals the presence of specific secreted candidate effector proteins expressed during apple infection. Unexpectedly, the survey of fungal unigenes in the transcriptome assemblies of inoculated and mock-inoculated apple leaves reveals that G. yamadae infection may modify the fungal community composition in the apple phyllosphere at 30 dpi. Collectively, our results provide novel insights into the compatible apple–G. yamadae interaction and advance the knowledge of this heteroecious demicyclic rust fungus.

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