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Whole-genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole-genome duplication (approximately 88 MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing on 10 collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and rediploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run-timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species. [ABSTRACT FROM AUTHOR]

Gene sequence similarity due to shared ancestry after a duplication event, that is 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 rediploidized 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 subtelomeric 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 rediploidization 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 rediploidization process. [ABSTRACT FROM AUTHOR]

How practical is gene and SNP discovery in a nonmodel species using short read sequences? Next-generation sequencing technologies are being applied to an increasing number of species with no reference genome. For nonmodel species, the cost, availability of existing genetic resources, genome complexity and the planned method of assembly must all be considered when selecting a sequencing platform. Our goal was to examine the feasibility and optimal methodology for SNP and gene discovery in the sockeye salmon ( Oncorhynchus nerka) using short read sequences. SOLiD short reads (up to 50 bp) were generated from single- and pooled-tissue transcriptome libraries from ten sockeye salmon. The individuals were from five distinct populations from the Wood River Lakes and Mendeltna Creek, Alaska. As no reference genome was available for sockeye salmon, the SOLiD sequence reads were assembled to publicly available EST reference sequences from sockeye salmon and two closely related species, rainbow trout ( Oncorhynchus mykiss) and Atlantic salmon ( Salmo salar). Additionally, de novo assembly of the SOLiD data was carried out, and the SOLiD reads were remapped to the de novo contigs. The results from each reference assembly were compared across all references. The number and size of contigs assembled varied with the size reference sequences. In silico SNP discovery was carried out on contigs from all four EST references; however, discovery of valid SNPs was most successful using one of the two conspecific references. [ABSTRACT FROM AUTHOR]