Cape dwarf-eelgrass genome assembly. Zostera capensis genome assembly and annotation

Seagrasses are integral marine bioengineers, providing numerous ecological services. In South Africa, the endangered Zostera capensis is the dominant seagrass species, although the populations of this species are heavily fragmented and are continuing to decline, driven by changing environmental conditions and anthropogenic pressures. To understand how this species may respond to environmental flux in the future, and provide guidance for the continued management of this important marine species, we assembled the first genome sequencing for Z. capensis, and used this genome to infer historic population expansion and contraction events through Pairwise Sequentially Markovian Coalescent (PSMC) modelling. Utilising a hybrid de novo assembly pipeline, a draft genome of 403 Mb was produced, with a BUSCO completeness score of 78%, adding to three available genome sequences for the Zostera genus. Additionally, the draft genome was annotated utilising available protein and transcriptomic data generated for Z. capensis and closely related species, utilising the nextflow genomeannotator pipeline. Furthermore, Pairwise Sequentially Markovian Coalescent (PSMC) analysis suggested historic population declines were significantly associated with sea level rise events, a scenario that is likely to reoccur in the coming years that will significantly impact genomic diversity of the species, limiting their adaptive potential. This genome represents a significant contribution to the limited genomic resources for Z. capensis, and provides important insight into potential demographic trends for management consideration.