Invasive Eurasian genotypes of the wetland grass Phragmites australis have colonized North America and are displacing native P. australis and other wetland species. Identifying molecular mechanisms that enhance competitive ability of invasive genotypes relative to native genotypes would have both basic and applied significance. Independently, 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 research, we determined whether invasive and native P. australis genotypes differed in their RNA expression profiles and transcriptional responses, and whether experimental inoculation by the Alternaria endophyte altered their transcriptional responses. 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 invasive and native 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
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. Based on fungal isolations from inoculated plants, experimental inoculations were 100% successful, and 96% of non-inoculated controls were free of Alternaria infection. In contrast to the invasive vs. native comparison, 569 loci were significantly differentially expressed in fungal inoculated vs. water-inoculated controls, with 495 upregulated and 74 downregulated. These results suggest that Alternaria endophyte inoculation had a relatively small effect on plant transcription compared to host invasion status. Pathways and GO terms analysis suggest differential expression of transcripts involved in growth (invasive vs. native) and plant defense (inoculated vs. control), but their functions in this system remain unclear. Our 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.