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Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

Qi Zhou12, Hong-mei Zhu3*, Quan-fei Huang3, Li Zhao1*, Guo-jie Zhang13, Scott W Roy4, Beatriz Vicoso2, Zhao-lin Xuan3, Jue Ruan2, Yue Zhang1, Ruo-ping Zhao1, Chen Ye3, Xiu-qing Zhang3, Jun Wang3*, Wen Wang1* and Doris Bachtrog2*

Author affiliations

1 CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

2 Department of Integrative Biology, University of California, Berkeley, CA 94720, USA

3 Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China

4 Department of Biology, Stanford University, Palo Alto, CA 94305, USA

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Citation and License

BMC Genomics 2012, 13:109  doi:10.1186/1471-2164-13-109

Published: 22 March 2012



Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.


We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.


We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.


Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.

Drosophila albomicans; neo-sex chromosome; B chromosome