The saltmarsh cordgrass Spartina anglica has novel genomic features that contribute to abiotic stress tolerance.

The allododecaploid cordgrass Spartina anglica thrives in saltmarshes, where it grows vigorously despite facing extreme environmental stresses. S. anglica was formed through a genome duplication of an infertile hybrid in ∼1870, and is today listed amongst 100 of the World's Worst Invasive Alien Species. Here we use long-read sequencing to provide a genomic sequence of S. anglica and undertake a detailed transcriptomic analysis of different S. anglica tissues. We demonstrate that S. anglica has undergone at least two whole genome duplication events and exhibits segmental allopolyploidy. We also show that S. anglica has evolved novel mechanisms to tolerate abiotic stress, including expansion and neofunctionalization of genes involved in sucrose synthesis, detoxification of reactive oxygen species and heavy metals, and calcium signalling associated with salt, ionic and nutrient stress. Furthermore, we demonstrate that S. anglica produces a diverse array of osmolytes, including dimethylsulfoniopropionate (DMSP), and reveal that a retrotransposon with a unique 55 bp insertion causes high-level expression of the DMSP-amine oxidase (DOX) gene and contributes to the exceptionally high levels of DMSP production in S. anglica. Together this work highlights the specialised genomic, transcriptomic and biochemical adaptations that S. anglica has evolved to tolerate severe abiotic stresses in saltmarshes.