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Open AccessResearch

Genomic degradation of a young Y chromosome in Drosophila miranda

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

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.


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