Abstract
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 eagle (Aquila chrysaetos) with no identified
chromosomes. The read depth per scaffold identified 86.41% of the
homogametic sex chromosome (Z) with few false positives. The SNP-loading
scores found 78.6% of the Z-chromosome but had a false positive
discovery rate of more than 10%. The heterozygosity per scaffold did
not provide clear results due to a lack of diversity in both the Z and
autosomal chromosomes, and potential interference from the heterogametic
sex chromosome (W).