Abstract

The rapid invasion of the non-native Phragmites australis (Poaceae, subfamily Arundinoideae) is a major threat to native ecosystems in North America. We describe a 1.14 Gbp reference genome for P. australis and compare invasive (ssp. australis) and native (ssp. americanus) genotypes collected across the Laurentian Great Lakes to deduce genomic bases driving its invasive success. We report novel genomic features including a lineage-specific whole genome duplication, followed by gene loss and preferential retention of genes associated with transcription factors and regulatory functions in the remaining duplicates. The comparative transcriptomic analyses revealed that genes associated with biotic stress and defense responses were expressed at a higher basal level in invasive genotypes, but the native genotypes showed a stronger induction of defense responses following fungal inoculation. The reference genome and transcriptomes, combined with previous ecological and environmental data, support the development of novel, genomics-assisted management approaches for invasive Phragmites.