Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)
Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)
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DOI：
10.1139/gen-2016-0202
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发表时间：
2017-09-01
期刊：
影响因子：
3.1
通讯作者：
Sork, Victoria L.
中科院分区：
文献类型：
--
作者：
Fitz-Gibbon, Sorel;Hipp, Andrew L.;Sork, Victoria L.
下一代测序技术的出现使遗传学数据量增加了几个数量级。减少代表性的方法，如限制性位点相关的DNA测序（RADseq），已被证明是有用的非模式物种的系统发育研究在广泛的系统发育深度。然而，对这些数据集的分析并不统一，我们对从头组装与通过映射到参考基因组的组装的潜在优点和缺点知之甚少。使用代表16个类群的83个橡树样本的RADseq数据，我们通过三个管道识别了变体：将序列读数映射到最近发表的野葛基因组草图，以及在两组位点过滤器下从头组装。对于每个管道，我们推断出最大似然概率。所有管道产生类似的树，在良好支持的分支内的关系有微小的变化，尽管它们产生不同数量的基因座（68 000 - 111 000个基因座）和不同程度的重叠与参考基因组。我们的结论是，参考对齐和从头组装管道产生可靠的结果，这些方法的优点和缺点主要涉及下游使用的RADseq数据，而不是系统发育推断本身。
The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-sited associated DNA sequencing (RADseq), have proven useful for phylogenetic studies of non-model species at a wide range of phylogenetic depths. However, analysis of these datasets is not uniform and we know little about the potential benefits and drawbacks of de novo assembly versus assembly by mapping to a reference genome. Using RADseq data for 83 oak samples representing 16 taxa, we identified variants via three pipelines: mapping sequence reads to a recently published draft genome of Quercus lobata, and de novo assembly under two sets of locus filters. For each pipeline, we inferred the maximum likelihood phylogeny. All pipelines produced similar trees, with minor shifts in relationships within well-supported clades, despite the fact that they yielded different numbers of loci (68 000 - 111 000 loci) and different degrees of overlap with the reference genome. We conclude that both the reference-aligned and de novo assembly pipelines yield reliable results, and that advantages and disadvantages of these approaches pertain mainly to downstream uses of RADseq data, not to phylogenetic inference per se.