Data from: Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

Gene sequence similarity due to shared ancestry after a duplication event, i.e. paralogy, complicates the assessment of genetic variation, as sequences originating from paralogs can be difficult to distinguish. These confounded sequences are often removed prior to further analyses, leaving the underlying loci uncharacterized. Salmonids have only partially re-diploidized subsequent to a whole-genome duplication; residual tetrasomic inheritance has been observed in males. We present a maximum likelihood-based method to resolve confounded paralogous loci by observing the segregation of alleles in gynogenetic haploid offspring and demonstrate its effectiveness by constructing two linkage maps for chum salmon (Oncorhynchus keta): with and without these newly resolved loci. We find that the resolved paralogous loci are not randomly distributed across the genome. A majority are clustered in expanded sub-telomeric regions of 14 linkage groups, suggesting a significant fraction of the chum salmon genome may be missed by the exclusion of paralogous loci. Transposable elements have been proposed as drivers of genome evolution and, in salmonids, may have an important role in the re-diploidization process by driving differentiation between homeologous chromosomes. Consistent with that hypothesis, we find a reduced fraction of transposable element annotations among paralogous loci, and these loci predominately occur in the genomic regions that lag in the re-diploidization process.