Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing.

The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g., Interior Alaska and St. Lawrence River have on average 181K and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 kbp and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g., amhby).

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.

Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.