BMC Seminar Thursday 16th of May at 12:00 in room 343 Læknagarður
Speaker: Charles C. R. Hansen, PhD student in Snæbjörn Pálssons research group, Department of Life and Environmental Sciences, University of Iceland
Title: Identification of the homogametic sex chromosome in non-model organisms
Abstract: Variation at the sex chromosomes and the mitochondrial genome is expected to differ from variation at the autosomal loci and for an assessment of genomic variation it is thus essential to evaluate the variation separately. Furthermore, evolution of the sex chromosomes and mtDNA can provide insights in to e.g. the evolutionary role of recombination, sex biased evolution and sexual differences in dispersal. But when working with non-model organisms the desired genome information is not always at hand, due to lack of prober or incomplete genomic references.
We evaluate and compare three methods for finding the homogametic sex chromosome, of a non-model organism, golden eagle (Aquila chrysaetos), by making use of genomic sequences of white-tailed eagle (Haliaeetus albicilla); two individuals (one of each sex) with a high coverage, RADSeq data from 144 individuals and a reference genome of golden eagle (with no sex chromosomes identified). Firstly, we map the golden eagle genome to the well assembled chicken reference genome. Secondly, we analyze the ratio of sequence coverage per scaffold between sexes; the coverage of scaffolds belonging to the Z chromosome in the heterogametic females should be ½ of the autosomal scaffolds. Lastly, we analyze the SNP-loading from a Principal Component Analysis of the RADSeq data.
Our analysis shows a high overlap when identifying Z chromosome scaffolds, using the mapping and coverage approaches, but it has proved harder to use SNP-loadings when using low depth data, with a high degree of missingness. But this problem too can be overcome.