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, 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.由复制事件后共享祖先所导致的基因序列相似性，即旁系同源（paralogy），会为遗传变异的评估带来干扰——因为源自旁系同源基因的序列往往难以区分。这类被混淆的序列通常会在后续分析前被移除，导致其对应的基因座无法得到解析。鲑科鱼类在经历全基因组复制后仅完成了部分二倍体化；目前已在雄性个体中观测到残留四体遗传现象。本研究提出一种基于最大似然（maximum-likelihood）的方法，通过观测雌核发育单倍体后代的等位基因分离情况，来解析被混淆的旁系同源基因座；并通过为大麻哈鱼（Oncorhynchus keta）构建两张连锁图谱（分别包含与不包含这些新解析的基因座），验证了该方法的有效性。研究结果显示，被解析的旁系同源基因座并非随机分布于整个基因组：其中绝大多数聚集于14个连锁群的扩增亚端粒区域，这表明若直接排除旁系同源基因座，大麻哈鱼基因组中有相当大的比例可能会被遗漏。转座因子（transposable elements）被认为是基因组演化的驱动因素；在鲑科鱼类中，其可能通过介导部分同源染色体间的分化，在二倍体化进程中发挥重要作用。与该假说相一致的是，本研究发现旁系同源基因座中转座因子注释的占比有所降低，且这类基因座主要集中在二倍体化进程较为滞后的基因组区域。