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首页> 外文期刊>BMC Genomics >Efficient high-throughput sequencing of a laser microdissected chromosome arm
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Efficient high-throughput sequencing of a laser microdissected chromosome arm

机译：激光显微切割染色体臂的高效高通量测序

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Background Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly. Results We laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly. Conclusion We present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds.
机译：背景基因组序列装配是广泛的基因功能和进化研究的关键工具。二倍体两栖类热带非洲爪蟾在这些领域中起着关键作用，这是由于它具有实验灵活性，二倍体基因组和早期分支的四足类生物分类位置的组合，它们已经与约3.6亿年前的羊膜血统背道而驰。基因组组装和遗传连锁图谱最近已经可用。不幸的是，连锁图谱中的大缺口削弱了基因组装配的远距离完整性。结果我们激光解剖了热带假单胞菌7号染色体的短臂，用于下一代测序和对参考基因组的计算作图。该臂特别有趣，因为它编码性别决定基因座，但其遗传图谱包含巨大的缺口，破坏了可用的基因组装配。对15个激光显微切割的7p臂进行全基因组扩增，然后进行下一代测序，产生了约3500万条读物，其中超过400万条独特地定位到了热带假单胞菌基因组。我们的分析在分析的染色体臂上放置了200多个以前未映射的支架，为从头基因组组装提供了有价值的低分辨率物理图谱信息。结论我们提出了一种改进和验证遗传图谱和序列装配的新方法。 15个微解剖的染色体臂的全基因组扩增为定位以前未映射的支架和基因以及识别错位的支架提供了足够的高质量材料。

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