Invasive Eurasian genotypes of the wetland grass Phragmites australis have colonized North America and are displacing native P. australis. Identifying genetic and molecular differences that allow invasive genotypes to outcompete native genotypes would have both basic and applied significance. In previous research on the fungal microbiome of invasive P. australis, we found that an endophytic fungus closely related to Alternaria alternata occurs at high prevalence across P. australis populations and plant tissue types, and is capable of vertical transmission through seeds. In this study, we aimed to determine whether invasive and native P. australis genotypes differ in their RNA expression profiles and transcriptional response to infection by the Alternaria endophyte. We grew 8 cuttings each from rhizomes of three North American native and three Eurasian invasive P. australis genotypes collected in the Great Lakes region, USA. One and two weeks after inoculating grown plants with the Alternaria endophyte (plus water-inoculated controls), we extracted RNA from leaf and rhizome tissue and generated over three billion RNA-seq reads from poly-A selected samples, which were then mapped to a P. australis reference genome.
Results/Conclusions
Based on fungal isolations from inoculated plants, experimental inoculations were 100% successful, and 96% of non-inoculated controls were free of Alternaria infection. In our highest sensitivity analysis, we identified 96,000 expressed loci. Of these, 16,663 loci were significantly differentially expressed in invasive vs. native P. australis at the 5% false discovery rate threshold, of which 11,974 were upregulated and 4,689 downregulated. In contrast, across all endophyte-inoculated plants, 569 loci were significantly differentially expressed, with 495 upregulated and 74 downregulated, suggesting that the Alternaria endophyte had a relatively small effect on plant transcription independent of host genotype. These results demonstrate that P. australis gene expression differs dramatically between native and invasive genotypes, with potential implications for understanding the underlying genetic mechanisms of invasive success. Important directions for future research include distinguishing between above- vs. below-ground plant responses and identifying the functional role of differentially expressed genes that may contribute to invasiveness.