Bachtrog, DorisHom, EmilyWong, Karen M.Maside Rodríguez, Xulio ManuelJong, Pieter de2021-01-212021-01-212008Bachtrog, D., Hom, E., Wong, K.M. et al. Genomic degradation of a young Y chromosome in Drosophila miranda. Genome Biol 9, R30 (2008). https://doi.org/10.1186/gb-2008-9-2-r301474-760Xhttp://hdl.handle.net/10347/24265Background: 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 patternseng© 2008 Bachtrog et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly citedhttp://creativecommons.org/licenses/by/2.0Bacterial Artificial ChromosomeBacterial Artificial Chromosome CloneBacterial Artificial Chromosome LibraryTransposable Element InsertionTransposable Element Abundancejournal article10.1186/gb-2008-9-2-r30open access