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

Area of Science:

• Evolutionary biology
• Genomics
• Ecology

Background:

• The Threespine Stickleback (Gasterosteus aculeatus) is a key model for studying adaptation due to repeated marine-to-freshwater transitions.
• Freshwater reference genomes may lack crucial genetic segments lost during adaptation, potentially biasing evolutionary studies.
• Cook Inlet, Alaska, offers natural replicates for studying this adaptive radiation.

Purpose of the Study:

• To create a high-quality marine genome assembly for Threespine Stickleback from Cook Inlet.
• To provide a more accurate ancestral reference genome for studying freshwater adaptation.
• To improve genomic analyses of marine-freshwater divergence in this species.

Main Methods:

• Generated a highly-continuous marine genome assembly using long-read sequencing.
• Ordered and oriented contigs using Hi-C technology.
• Anchored contigs to chromosomes, resulting in a 454 Mbp assembly with high contiguity and completeness.

Main Results:

• A 454 Mbp marine genome assembly with an N50 of 1.3 Mbp and BUSCO score >97% was produced.
• The marine assembly revealed structural differences, including three inversions, compared to freshwater assemblies.
• This assembly includes genomic segments often lost in freshwater populations.

Conclusions:

• The new marine assembly serves as a more accurate reference for the ancestral population that colonized local freshwater lakes.
• It will facilitate more comprehensive genomic studies of Threespine Stickleback adaptation and evolution worldwide.
• This resource enhances the utility of Threespine Stickleback as a model for understanding vertebrate adaptation.