The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.
The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.
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DOI：
10.1534/genetics.115.174664
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发表时间：
2015-04
期刊：
影响因子：
3.3
通讯作者：
Pool JE
中科院分区：
文献类型：
--
作者：
Lack JB;Cardeno CM;Crepeau MW;Taylor W;Corbett-Detig RB;Stevens KA;Langley CH;Pool JE
已经发表了数百个野生黑腹果蝇基因组，但由于比对方法的差异，无法对数据集进行严格的比较。基于参考的基因组组装最常见的方法是单轮比对，然后进行质量过滤和变异检测。我们评估了这种方法的变化和扩展，并确定了一种组装策略，该策略利用两个比对程序，并结合了替换和短插入缺失，以在最终变异检测之前构建第二轮映射的更新参考。利用这种方法，我们重新组装发表的D。黑腹果蝇种群基因组数据集，并添加了来自撒哈拉以南几个种群的未发表的基因组。最值得注意的是，我们提出了来自果蝇种群基因组学计划（DPGP3）第3阶段的对齐数据，该计划提供了来自果蝇单一祖先范围种群的197个基因组。产自赞比亚。DPGP3样本的大样本量，高遗传多样性和可能更简单的人口统计学历史将使其成为基础人群遗传学研究的极有价值的资源。这里描述的一整套组件，称为果蝇基因组连接，目前包括623个一致对齐的基因组，并以多种格式公开提供支持文档和生物信息学工具。该资源将通过减少数据集之间的方法差异，极大地促进该模式物种的种群基因组分析。
Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets.