Genomic degradation of a young Y chromosome in Drosophila miranda

Doris Bachtrog¹ , Emily Hom¹ , Karen M Wong¹ , Xulio Maside²^,4 and Pieter de Jong³

¹Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA

²Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK

³Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA

⁴Current address: Grupo de Medicina Xenómica, Instituto de Medicina Legal, CIBERER, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain

author email corresponding author email

Genome Biology 2008, 9:R30doi:10.1186/gb-2008-9-2-r30


Published:	12 February 2008

Subject areas: Evolution, Genetics, Genome studies

Abstract

Background

Y chromosomes are derived from ordinary autosomes and degenerate because of a lack of recombination. Well-studied Y chromosomes only have few of their original genes left and contain little information about their evolutionary origin. Here, we take advantage of the recently formed neo-Y chromosome of Drosophila miranda to study the processes involved in Y degeneration on a genomic scale.

Results

We obtained sequence information from 14 homologous bacterial artificial chromosome (BAC) clones from the neo-X and neo-Y chromosome of D. miranda, encompassing over 2.5 Mb of neo-sex-linked DNA. A large fraction of neo-Y DNA is composed of repetitive and transposable-element-derived DNA (20% of total DNA) relative to their homologous neo-X linked regions (1%). The overlapping regions of the neo-sex linked BAC clones contain 118 gene pairs, half of which are pseudogenized on the neo-Y. Pseudogenes evolve significantly faster on the neo-Y than functional genes, and both functional and non-functional genes show higher rates of protein evolution on the neo-Y relative to their neo-X homologs. No heterogeneity in levels of degeneration was detected among the regions investigated. Functional genes on the neo-Y are under stronger evolutionary constraint on the neo-X, but genes were found to degenerate randomly on the neo-Y with regards to their function or sex-biased expression patterns.

Conclusion

Patterns of genome evolution in D. miranda demonstrate that degeneration of a recently formed Y chromosome can proceed very rapidly, by both an accumulation of repetitive DNA and degeneration of protein-coding genes. Our data support a random model of Y inactivation, with little heterogeneity in degeneration among genomic regions, or between functional classes of genes or genes with sex-biased expression patterns.