| Summary: | Genomic variation is the key to speciation and evolution. Genomic variants underlie how species change, adapt, and evolve and range from single-point mutations to large chromosomal rearrangements. Inversions are an example of the latter and can profoundly affect local adaptation, such as with the Atlantic cod. The Atlantic cod that inhabit the northernmost coast of Norway consists of two ecotypes: the stationary Northern Coastal Cod (NCC) and the migratory Northeast Arctic Cod (NEAC), which feeds offshore in the Barents Sea and only returns to the Northern coast to breed. NCC and NEAC breed at the same time and locations along the coast of Norway, from Møre in the south to Sørøya in the north, with the largest spawning aggregation taking place around the Lofoten archipelago. Even though they spawn simultaneously, phenotypic, and genetic differences are maintained between the two populations. From previous studies, four megabase-scale supergenes have been linked to migratory lifestyle and environmental adaptations, and I set out to locate the breakpoints and determine if they vary between individuals. To do so, I developed a PCR protocol for amplifying both inverted and non-inverted alleles to sequence the breakpoint regions within the Atlantic cod. In total, 79 breakpoint regions were sequenced using HiFi-sequencing, which creates accurate long reads known as HiFi reads. In doing so, I could use multiple, accurate, HiFi sequencing reads to (1) align each breakpoint read to the gadmor3 and coastal reference genome and then (2) make de novo haplotype assemblies for the breakpoint regions for different individuals with the inverted and non-inverted allele. The haplotype assemblies were used in a multiple sequence alignment, and I could pinpoint where the breakpoints are and that they are conserved and fixed within and between populations.
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