Finding stories in noise: Mitochondrial portraits from RAD data
Finding stories in noise: Mitochondrial portraits from RAD data
复制标题
在噪音中寻找故事：RAD 数据中的线粒体肖像
DOI：
--
复制
发表时间：
2018
影响因子：
7.7
通讯作者：
P. Bloomer
中科院分区：
文献类型：
--
作者：
Cora S. Stobie;M. Cunningham;C. Oosthuizen;P. Bloomer
线粒体DNA（mtDNA）多年来一直是生物地理学研究的支柱;然而，最近的趋势集中在全基因组分析上。提出的一种用于校准来自噪声下一代数据的推断的方法，例如RAD测序，是将这些结果与线粒体序列的分析进行比较。大多数使用这种方法的研究人员似乎没有意识到，从全基因组序列数据中鉴定出的许多单核苷酸多态性（SNP）本身就是线粒体，或者认为这些SNP太少而无法进行偏倚分析。在这里，我们展示了两种方法，使用RAD序列数据从三个南非种的黄鱼，Labeobarbus的线粒体标记挖掘。首先，我们使用严格的SNP发现管道，使用程序堆栈，以确定mtDNA中的变异位点，然后我们将其联合收割机组合成单倍型。第二，我们直接将序列读数映射到线粒体基因组参考。这种方法使我们能够重建高达98%的Labeobarbus有丝分裂基因组。我们通过blast数据库搜索和通过与通过桑格测序获得的细胞色素B基因序列比较来验证这些有丝分裂基因组重建。最后，我们调查了这些数据的生物后果，包括古老的遗传交换和最近的易位之间的人口L。natalensis之间的种间杂交以及L. aeneus和L.金伯利
Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome‐wide analyses. One method proposed for calibrating inferences from noisy next‐generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many single nucleotide polymorphisms (SNPs) identified from genome‐wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses. Here, we demonstrate two methods for mining mitochondrial markers using RAD sequence data from three South African species of yellowfish, Labeobarbus. First, we use a rigorous SNP discovery pipeline using the program stacks, to identify variant sites in mtDNA, which we then combine into haplotypes. Second, we directly map sequence reads against a mitochondrial genome reference. This method allowed us to reconstruct up to 98% of the Labeobarbus mitogenome. We validated these mitogenome reconstructions through blast database searches and by comparison with cytochrome b gene sequences obtained through Sanger sequencing. Finally, we investigate the organismal consequences of these data including ancient genetic exchange and a recent translocation among populations of L. natalensis, as well as interspecific hybridization between L. aeneus and L. kimberleyensis.
影响因子：
7
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
通讯作者：
Johnson, Eric A.