Distilling artificial recombinants from large sets of complete mtDNA genomes.
Distilling artificial recombinants from large sets of complete mtDNA genomes.
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DOI：
10.1371/journal.pone.0003016
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发表时间：
2008-08-20
期刊：
影响因子：
3.7
通讯作者：
Bandelt HJ
中科院分区：
文献类型：
--
作者：
Kong QP;Salas A;Sun C;Fuku N;Tanaka M;Zhong L;Wang CY;Yao YG;Bandelt HJ
大规模基因组测序给实验室工作的后勤和数据处理带来了巨大的问题。当不同基因组的许多片段在实验室进行PCR扩增和测序时，存在很高的样本混淆风险。对于遗传标记，如线粒体DNA (mtDNA)，没有自然重组，涉及mtDNA系统发育的不同分支的样品混淆的单个实例将产生网状模式，因此应该是可检测的。我们已经开发了一种策略，将新的完整mtDNA基因组一个接一个地与全球mtDNA系统发育的当前骨架进行比较。区分参考序列和推定重组序列的突变可以被分配到该系统发育骨架的两个或多个不同分支。因此，人们将在整个mtDNA数据库中寻找两个（或三个）接近匹配的dna，它们加在一起最能解释重组中所见的变异。mtDNA树的进化路径将这对基因与重组基因连接在一起，然后产生一个网格状的中间网络，从中可以读出交换的片段。我们已经将此程序应用于大量完整的人类mtDNA序列，其中一些重组可以通过我们的方法进行提取。所有这些重组序列随后都通过从头实验进行了修正-与我们的数据分析方法的预测完全一致。
Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high immanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable. We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments. We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments – fully concordant with the predictions from our data-analytical approach.
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影响因子：
4.1
作者：
Bandelt, HJ;Macaulay, V;Richards, M
通讯作者：
Richards, M
影响因子：
14.9
作者：
Gajer, P;Schatz, M;Salzberg, SL
通讯作者：
Salzberg, SL
DOI：
10.1016/j.bbrc.2005.04.055
发表时间：
2005-07-22
影响因子：
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作者：
Bandelt, HJ;Achilli, A;Yao, YG
通讯作者：
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影响因子：
2.1
作者：
Bandelt, HJ;Salas, A;Lutz-Bonengel, S
通讯作者：
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影响因子：
2.1
作者：
Bandelt, HJ;Lahermo, P;Macaulay, V
通讯作者：
Macaulay, V