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 inf...
| Main Authors: | , , |
|---|---|
| Format: | Dataset |
| Language: | English |
| Published: |
Dryad
2021
|
| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.v9s4mw6vs https://datadryad.org/stash/dataset/doi:10.5061/dryad.v9s4mw6vs |
| Summary: | 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) ... : Blood samples were collected from white-tailed eagle chicks as a part of an ongoing monitoring program in Iceland since 2001 by the Natural History Institute of Iceland. The sex of the chicks was determined in the field based on morphology. Three to ten mL of blood was extracted from each chick. The blood was stored in EDTA buffer at -20 degrees until DNA extraction. DNA from blood samples from 133 chicks were extracted using the ThermoFisher GeneJET Whole Blood Genomics DNA Purification Mini Kit following the standard protocol (Thermo Fisher, 2016). DNA concentration was estimated using the NanoDrop 1000 and run on 0.7% agarose gels to evaluate the fragment size. Samples with concentration higher than 60 ng/µl were selected for library preparation and sequencing. The 133 samples were prepared for double digest restriction-site associated DNA sequencing (ddRADseq) using modified protocols from Elshire et al. (2011) and Peterson et al. (2012). Total genomic DNA (100-500 ng) was sequentially digested using the ... |
|---|