Abstract
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear–cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.
Highlights
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes
We find no evidence for functional differentiation of the 46 genes identified on the W chromosome, all of which have a gametologous copy on the Z chromosome
A comparison with the gene content of the flycatcher Z chromosome revealed that all non-recombining region of the W chromosome (NRW) genes have a gametologous copy on the Z chromosome
Summary
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. The nuclear genome of sexually reproducing animals is shared between males and females and is affected by evolutionary processes pertinent to both sexes This comes with the exception of the non-recombining part of the sex-limited chromosome, that is, the Y chromosome in male heterogametic organisms (females XX, males XY) and the W chromosome in female heterogametic organisms (females ZW, males ZZ), where sequence evolution reflects processes specific to one sex. Transmission through oogenesis rather than spermatogenesis implies that W chromosomes are exposed to a different mutational and epigenetic germ line environment than Y chromosomes How these and other factors affect W chromosome evolution are largely unknown and the lack of large-scale polymorphism data has hindered population genomic analyses of W-linked sequences. We demonstrate complete matrilineal co-inheritance of the W chromosome and mitochondrial DNA
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