title: Identification of avian W-linked contigs by short-read sequencing.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA. nc276@cornell.edu
authors.forename: Nancy
authors.initials: N
authors.lastname: Chen
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Bellott
authors.forename: David C
authors.initials: DC
authors.lastname: Page
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Clark
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D020451:Contig Mapping / Q000379:methods*; D005260:Female; D008297:Male; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012730:Sex Chromosomes / Q000235:genetics*