Evaluation of four methods to identify the homozygotic sex chromosome in small populations

Whole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes and, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types can have highly disparate evolutionary histories, it is imperative to take this information into account when analyzing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome using two whole genome sequenced (WGS) and 133 RAD sequenced white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold, ii) heterozygosity per scaffold in a male and female bird, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) an analysis of SNP-loadings from a principal components analysis (PCA), based on low-depth RADseq data from 133 individuals. In i and ii, the WGS were mapped to a reference genome consisting of 1142 assembled scaffolds from the golden eagl...

全基因组通常被组装为一系列支架序列（scaffold），且往往未对常染色体、性染色体以及细胞器基因组（即线粒体基因组与叶绿体基因组）进行注释。由于不同染色体类型的进化历史存在显著差异，在分析基因组变异时必须将这一特征纳入考量。本研究以2只经全基因组测序（Whole Genome Sequencing, WGS）的个体与133只经限制性酶切位点相关DNA测序（Restriction-site Associated DNA Sequencing, RADseq）的白尾海雕（*Haliaeetus albicilla*）为研究对象，评估了4种鉴定同配性别性染色体的方法的准确性：（i）各支架序列的测序reads深度差异；（ii）雌雄个体各支架序列的杂合度水平；（iii）将测序数据比对至已明确注释性染色体的近缘物种（鸡）参考基因组；（iv）基于133个个体的低深度RADseq数据，通过主成分分析（Principal Components Analysis, PCA）的SNP载荷值开展分析。在方法i和ii中，全基因组测序数据被比对至由1142个组装得到的支架序列所构成的参考基因组，该参考基因组来自金雕（golden eagl）...