Transcriptome-based analyses of phosphite-mediated suppression of rust pathogens Puccinia emaculata and Phakopsora pachyrhizi

We explored the use of Phi in controlling the fungal pathogens Puccinia emaculata and Phakopsora pachyrhizi, the causal agents of switchgrass rust and Asian soybean rust, respectively. RNA sequencing of both the pathogens with and without treatment with Phi was conducted. Differentially expressed genes were identified in both pathogens and comparison of differentially expressed genes was made to identify commonly regulated genes by Phi. Total RNA from Phi-treated Pe and Pp was isolated using an RNeasy plant mini kit (Qiagen). Two biological replicates were used for each treatment (12 samples). Illumina TruSeq sequencing-by-synthesis chemistry was used on a HiSeq 2000 platform (Illumina, https://www.illumina.com/) to generate paired-end reads (2 × 100 bp). Overall design: Urediniospores of Pe and Pp were dusted on 1× germination solution [500× stock: 0.0036% nonanol (v/v), 0.025% Tween 20 (v/v), 50% ethanol (v/v), in autoclaved distilled water] supplemented with 0, 10 or 100 mM Phi on a Petri plate. Urediniospores were allowed to germinate for 24 h in the dark. After 24 h, germinated urediniospores were collected by skimming them from the surface of the solution with the help of a cover slip.