State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.
Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telengana, India.
DNA Res. 2018 Aug 1;25(4):375-382. doi: 10.1093/dnares/dsy010.
Notwithstanding the rapid developments in sequencing techniques, Y and W sex chromosomes have still been mostly excluded from whole genome sequencing projects due to their high repetitive DNA content. Therefore, Y and W chromosomes are poorly described in most species despite their biological importance. Several methods were developed for identifying Y or W-linked sequences among unmapped scaffolds. However, it is not enough to discover functional regions from short unmapped scaffolds. Here, we provide a new and simple strategy based on k-mer comparison for comprehensive analysis of the W chromosome in Bombyx mori. Using this novel method, we effectively assembled de novo 1281 W-derived genome contigs (totaling 1.9 Mbp), and identified 156 W-linked transcript RNAs and 345 W-linked small RNAs. This method will help in the elucidation of mechanisms of sexual development and exploration of W chromosome biological functions, and provide insights into the evolution of sex chromosomes. Moreover, we showed this method can be employed in identifying heterogametic sex chromosomes (W and Y chromosomes) in many other species where genomic information is still scarce.
尽管测序技术发展迅速，但由于 Y 和 W 性染色体的高度重复 DNA 含量，它们仍然大多被排除在全基因组测序项目之外。因此，尽管 Y 和 W 染色体具有重要的生物学意义，但大多数物种对它们的描述仍然很差。已经开发了几种方法来识别未映射支架中的 Y 或 W 连锁序列。然而，仅从短的未映射支架中发现功能区域是不够的。在这里，我们提供了一种新的基于 k-mer 比较的简单策略，用于全面分析家蚕的 W 染色体。使用这种新方法，我们有效地从头组装了 1281 个 W 衍生的基因组 contigs（总计 1.9 Mbp），并鉴定了 156 个 W 连锁转录 RNA 和 345 个 W 连锁小 RNA。该方法将有助于阐明性发育的机制，并探索 W 染色体的生物学功能，为性染色体的进化提供了线索。此外，我们表明，该方法可用于鉴定基因组信息仍然稀缺的许多其他物种中的异型性染色体（W 和 Y 染色体）。
