Abstract
Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy simultaneously are of particular interest, as understanding the mechanisms that maintain this mosaic of ploidy after WGDs may provide important insights into evolutionary processes. Salmonids are a useful model to study the effect of WGDs due to the extensive diversity that has evolved following an ancestral autotetraploidization event. Although most of the salmonid genome has reverted to diploidy following WGD, approximately 25% of the chromosomes continue to exist in a state of residual tetrasomy. In this study, we generate a novel linkage map for cisco (Coregonus artedi) and conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. Additionally, we propose a new naming strategy, protokaryotypes, that facilitates comparisons across Salmonids by standardizing naming to ancestral chromosomes from northern pike (Esox lucius). The female linkage map for cisco contains 20,450 loci, 3,383 of which are likely contained within residually tetraploid regions of the genome. Comparative genomic analysis revealed that patterns of residual tetrasomy are generally conserved across species, but there is interspecific variation in the relative extent of the residual tetrasomy. Additionally, with the current reference genomes available, we only find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.
Footnotes
Data deposition: Raw sequence data has been uploaded to SRA under BioProject PRJNA555579
