Even in organisms like Drosophila melanogasterwhere the quality of the whole genome shotgun assembly is extremely high, the Y chromosome remains a collection of unassembled contigs [ 7 - 9 ]. Known W contigs are shown in red, known Z or autosomal contigs are in blue, and unmapped contigs are in gray.
Mutant alleles of sex determination genes have been combined to create dioecious and trioecious strains Cutter ; Stewart and Phillips
Figure 1. It has no tRNA genes, and fewer conserved genes were found on the X compared to the autosomes. To account for differences in mutation rate, comparisons of diversity between X and the autosomes have relied on normalization of each by divergence from an outgroup 1,2,8 as described above.
Estimates of Nucleotide Diversity We used the final filtered set of SNPs and genomic regions from X and the autosomes to build a collection of kb loci defined by grouping bases along chromosomes that did not meet any of the above filtering criteria, i. We used bootstrap replicates to estimate confidence intervals of mean coverage and read depth for known autosomal or Z-linked contigs, which were then compared to the coverage and read depth values, respectively, of each putative W-specific contig.
Genomic Regions and Filters To obtain what two sex chromosomes do males have a y in Coventry set of SNPs and regions used in the analysis, we applied several genomic and data-quality filters to minimize sequencing, alignment, variant inference, and genomic assembly errors, as well as to exclude candidate regions under the direct influence of selective constraints.
To explore the origins of the changed complement of chromosomes and reduced size, we aligned the A.
Show less. Our pipeline relies on the subtraction of the male genome from the female genome and tests for lower read depth on a contig-by-contig basis. Because the X chromosome is repressed in germ cells, the X:A ratio steadily declines as the individual develops Deng et al.
Because we used only one library, there was no reason to calculate RPKM, which standardizes among libraries. The female vs.