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Open Access Methodology article

Identification of avian W-linked contigs by short-read sequencing

Nancy Chen12*, Daniel W Bellott3, David C Page3 and Andrew G Clark14

Author Affiliations

1 Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA

2 Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, New York, USA

3 Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts, USA

4 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA

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BMC Genomics 2012, 13:183  doi:10.1186/1471-2164-13-183

Published: 14 May 2012



The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific to these sex chromosomes. Here, we develop and apply a novel method for identifying sequences that are W-specific.


Using the Illumina Genome Analyzer, we generated sequence reads from a male domestic chicken (ZZ) and mapped them to the existing female (ZW) genome sequence. This method allowed us to identify segments of the female genome that are underrepresented in the male genome and are therefore likely to be female specific. We developed a Bayesian classifier to automate the calling of W-linked contigs and successfully identified more than 60 novel W-specific sequences.


Our classifier can be applied to improve heterogametic whole-genome shotgun assemblies of the W or Y chromosome of any organism. This study greatly improves our knowledge of the W chromosome and will enhance future studies of avian sex determination and sex chromosome evolution.

Sex chromosomes; Next-generation sequencing