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Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes

Qi Zhou12, Jun Wang345, Ling Huang26, Wenhui Nie6, Jinhuan Wang6, Yan Liu26, Xiangyi Zhao1, Fengtang Yang7* and Wen Wang1*

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 (CAS), 32# Jiao-chang Road, Kunming, Yunnan 650223, People's Republic of China

2 Graduate School of Chinese Academy Sciences, 19# Yu-quan Road, Beijing 100039, People's Republic of China

3 The Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark

4 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark

5 Beijing Genomics Institute, Bei-shan Road, Shenzhen 518083, People's Republic of China

6 Kunming Cell Bank, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32# Jiao-chang Road, Kunming, Yunnan 650223, People's Republic of China

7 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Ickleton Road, Hinxton, Cambridge, CB10 1SA, UK

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Genome Biology 2008, 9:R98  doi:10.1186/gb-2008-9-6-r98

Published: 14 June 2008

Abstract

Background

The regular mammalian X and Y chromosomes diverged from each other at least 166 to 148 million years ago, leaving few traces of their early evolution, including degeneration of the Y chromosome and evolution of dosage compensation.

Results

We studied the intriguing case of black muntjac, in which a recent X-autosome fusion and a subsequent large autosomal inversion within just the past 0.5 million years have led to inheritance patterns identical to the traditional X-Y (neo-sex chromosomes). We compared patterns of genome evolution in 35-kilobase noncoding regions and 23 gene pairs on the homologous neo-sex chromosomes. We found that neo-Y alleles have accumulated more mutations, comprising a wide variety of mutation types, which indicates cessation of recombination and is consistent with an ongoing neo-Y degeneration process. Putative deleterious mutations were observed in coding regions of eight investigated genes as well as cis-regulatory regions of two housekeeping genes. In vivo assays characterized a neo-Y insertion in the promoter of the CLTC gene that causes a significant reduction in allelic expression. A neo-Y-linked deletion in the 3'-untranslated region of gene SNX22 abolished a microRNA target site. Finally, expression analyses revealed complex patterns of expression divergence between neo-Y and neo-X alleles.

Conclusion

The nascent neo-sex chromosome system of black muntjacs is a valuable model in which to study the evolution of sex chromosomes in mammals. Our results illustrate the degeneration scenarios in various genomic regions. Of particular importance, we report - for the first time - that regulatory mutations were probably able to accelerate the degeneration process of Y and contribute to further evolution of dosage compensation.