Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.
BMC Genomics. 2012 May 14;13:183. doi: 10.1186/1471-2164-13-183.
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.
女性特有的 W 染色体和男性特有的 Y 染色体很难通过全基因组鸟枪法进行组装，这就需要新的方法来鉴定这些性染色体特有的序列片段。在这里，我们开发并应用了一种鉴定 W 染色体特异性序列的新方法。
我们使用 Illumina Genome Analyzer 从一只雄性家鸡（ZZ）中生成了序列读数，并将其映射到现有的雌性（ZW）基因组序列上。这种方法使我们能够鉴定出在雄性基因组中代表性不足的雌性基因组片段，因此这些片段很可能是雌性特异性的。我们开发了一种贝叶斯分类器来自动鉴定 W 连锁的基因组片段，并成功鉴定出了 60 多个新的 W 染色体特异性序列。
我们的分类器可用于改进任何生物体的 W 或 Y 染色体异配子全基因组鸟枪法组装。本研究极大地提高了我们对 W 染色体的认识，并将增强未来对鸟类性别决定和性染色体进化的研究。
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