Genomic and transcriptomic sequencing of the saltmarsh cordgrass Spartina anglica reveals novel adaption mechanisms for abiotic stress tolerance

The allododecaploid cordgrass Spartina anglica thrives in saltmarshes, where it grows vigorously despite facing extreme environmental stresses such has high salinity, waterlogging, heavy metals and low-redox conditions. S. anglica was formed through a genome duplication of an infertile hybrid in ~1870, and today it is considered a highly invasive species and is listed amongst 100 of the Worlds 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 leaf, stem, inflorescence, root, and rhizome 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. We demonstrate that S. anglica also produces a diverse array of osmolytes, including dimethylsulfoniopropionate (DMSP), and reveal that DMSP production occurs at exceptionally high levels in S. anglica because of a unique retrotransposon that causes high-level expression of the DMSP-amine oxidase (DOX) gene. Together this work highlights the various specialised genomic, transcriptomic and biochemical adaptations that S. anglica has evolved to tolerate severe abiotic stresses in the saltmarsh.