Genome assembly of Spinifex sericeus provides insights into repetitive content and haplotype variation in a dioecious coastal grass

Abstract

Spinifex sericeus (beach spinifex) is a perennial, dioecious grass native to coastal ecosystem of Oceania that has an important role in dune stability. We present a near telomere-to-telomere, haplotype-resolved nuclear genome alongside complete organelle genomes of S. sericeus. The nuclear genome is highly repeat-rich, dominated by long terminal repeat (LTR) retrotransposons. Comparative analysis of the two haplotypes reveals extensive structural variation and high levels of duplication that are suggestive of active and expanding LTRs that may drive genome evolution and expansion in this species. The chloroplast genome exhibits heteroplasmy, having two distinct circular configurations spanning 138 kbp each. The complex mitochondrial genome consists of a large linear component spanning 1.85 Mbp and a small circular 134 kbp component. These genomic resources provide a foundation for advancing research on sex determination and stress adaptation in grasses, and well as practical applications in crop improvement and genetically informed coastal dune restoration. Significance statementThe reference genome of Spinifex sericeus provides a foundational resource for understanding adaptations to the harsh coastal dune environment, including saline conditions, extreme temperatures, and drought. The genome enables comparative studies within Poaceae, where current reference genomes are dominated by crop species, and supports conservation and restoration efforts for coastal ecosystem management.