Genome Sequence of a Marine Threespine Stickleback () from Rabbit Slough in the Cook Inlet.

The Threespine Stickleback, , 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. These replicates have enabled researchers to efficiently identify phenotypes and genotypes under selection during this transition. While this repeated adaptation to freshwater has occurred throughout the northern hemisphere, the Cook Inlet in south-central Alaska has been an area of focus. The freshwater lakes in this area are being studied extensively and 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 freshwater adaptation. This scenario results in some of the key regions associated with marine-freshwater divergence being absent from freshwater genomes, and therefore absent from the reference assemblies. It may also be that isolated freshwater populations are more genetically diverged, potentially increasing reference biases. Here we present a highly-continuous marine assembly from Rabbit Slough in the Cook Inlet. All contigs are from long-read sequencing and have been ordered and oriented with Hi-C. The contigs 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 over 97%. The organization of the chromosomes in this marine individual is similar to existing freshwater assemblies, but with important structural differences, including the 3 previously known inversions that repeatedly separate marine and freshwater ecotypes. We anticipate that this high-quality marine assembly will more accurately reflect the ancestral population that founded the freshwater lakes in the area and will more closely match most other populations from around the world. This marine assembly, which includes the 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.