Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet.

The threespine stickleback, Gasterosteus aculeatus, is an emerging model system for understanding the genomic basis of vertebrate adaptation. A strength of the system is that marine populations have repeatedly colonized freshwater environments, serving as natural biological replicates. While repeated adaptation to freshwater has occurred throughout the northern hemisphere, Cook Inlet in south-central Alaska has been an area of focus. There is a high-quality freshwater reference assembly from a population in the region, Bear Paw Lake. Using a freshwater reference assembly is a potential limitation because genomic segments are repeatedly lost during adaptation to freshwater. Thus, some of the key regions associated with marine-freshwater divergence are absent from freshwater genomes, and therefore absent from the reference assemblies. Here, we present a highly continuous assembly from the marine population that breeds in (anadromous) Rabbit Slough in Cook Inlet. All contigs are from long-read sequencing and have been ordered and oriented with Hi-C. They are anchored to chromosomes and form a 454 Mbp assembly with an N50 of 1.3 Mbp, an L50 of 95, and a BUSCO score greater than 97%. We expect this high-quality marine assembly to more accurately reflect the ancestral genome of the marine stickleback that founded populations in freshwater habitats in the area and will more closely match most other populations from around the world. This marine assembly, which includes repeatedly deleted segments and offers a closer reference sequence for most populations, will enable more comprehensive and accurate computational and functional genomic investigations of threespine stickleback evolution.