Data from: Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping by sequencing data from natural populations

Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: 1) the expected frequency of heterozygotes exceeds that for singleton loci, and 2) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci. These deviations are often not apparent within individuals, particularly when sequence coverage is low; but, we postulated that summing allele reads for each locus over all heterozygous individuals in a population would provide sufficient power to detect deviations at those loci. We identified paralogous loci in three species: Chinook salmon (Oncorhynchus tshawytscha) which retains regions with ongoing residual tetrasomy on eight chromosome arms following a recent whole genome duplication, mountain barberry (Berberis alpina) which has a large proportion of paralogs that arose through an unknown mechanism, and dusky parrotfish (Scarus niger) which has largely re-diploidized following an ancient whole genome duplication. Importantly, this approach only requires the genotype and allele-specific read counts for each individual, information which is readily obtained from most GBS analysis pipelines.全基因组复制（whole genome duplication）事件曾发生于众多植物、鱼类与两栖动物的近期祖先类群中，由此导致旁系同源基因座（paralogous loci）广泛存在，并使得同一基因组内同时具备二体遗传与四体遗传的潜在可能。旁系同源基因座往往难以实现可靠的基因分型，且常被排除在测序分型（genotyping-by-sequencing，GBS）分析之外；然而，要移除这类基因座，首先需要对其进行识别，而在缺乏参考基因组（reference genome）的情况下，这一过程极具挑战性。我们提出了一种可在自然种群中识别旁系同源基因座的方法，该方法结合了重复基因座的两项核心特征：其一，杂合子（heterozygotes）的预期出现频率高于单拷贝基因座（singleton loci）；其二，在GBS数据的杂合个体中，每个等位基因的观测读取比例会偏离二倍体单拷贝基因座所预期的1:1比例。这类偏差通常难以在单个个体中被检测到，尤其是在测序覆盖度（sequence coverage）较低的情况下；但我们推测，将种群中所有杂合个体的某一基因座的等位基因读取数进行汇总，便可获得足够的统计效力以识别这类基因座的偏差。我们在三个物种种群中完成了旁系同源基因座的识别：一是奇努克鲑（Oncorhynchus tshawytscha），其在近期发生全基因组复制后，八条染色体臂上仍保留有持续存在的残留四体性区域；二是山小檗（Berberis alpina），该物种中存在大量由未知机制产生的旁系同源基因座；三是暗绿鹦嘴鱼（Scarus niger），其在古老全基因组复制事件后已基本完成重新二倍体化。值得注意的是，本方法仅需每个个体的基因型数据与等位基因特异性读取计数（allele-specific read counts），而这类信息可从绝大多数GBS分析流程中便捷获取。