Two Australian genome assemblies expand the genomic blueprint of giant kelp

Giant kelp, Macrocystis pyrifera (order Laminariales), occurs across the temperate coasts of the Northern and Southern Hemispheres and is at high risk from ocean warming. Few giant kelp forests remain across the Southeast Australian shelf, and some sites are currently under active restoration. Genomic resources can greatly aid in the conservation of remnant populations and enhance restoration efforts. Reference genomes are a fundamental resource as they are either prerequisites for, or substantially improve, many analyses used in conservation genomics. A single reference genome is available for giant kelp, assembled from a Californian haploid specimen. However, increasing evidence of genetic divergence between Northern and Southern Hemisphere populations highlights the need for regionally representative reference genomes.

We present two genome assemblies from the vegetative tissue (diploid sporophyte) of Australian giant kelp specimens. We performed de novo genome assembly using long-read sequencing (PacBio HiFi and ONT R10.4 Simplex) and used the ONT reads for scaffolding, assembling 98-99% of the genomes into 35 pseudo-chromosomes. Genome sizes ranged from 528 to 534 Mbp, with BUSCO completeness of 96-97% and QV scores of 51-52. Functional annotation identified 17,330 - 17,832 genes in the Australian assemblies. Genomic divergence between Australian and Californian genomes was seven-fold greater than between Australian genomes (1.5% vs. 0.2%), supporting a northeast-southwest Pacific genetic divergence. Differences in gene ontology enrichment patterns were also observed between Australian and Californian genomes, reflected by differing patterns of enrichment in gene ontologies linked to energy metabolism, proteostasis and stress responses.

These two new genome assemblies will serve as valuable resources for ongoing research into Australian giant kelp genetics, while providing the basis for genomics-guided conservation and restoration of remnant giant kelp forests in Australia.