Distilling artificial recombinants from large sets of complete mtDNA genomes

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	Distilling artificial recombinants from large sets of complete mtDNA genomes
	Kong QP 1,2; Salas A 3; Sun C 1; Fuku N 4; Tanaka M 4; Zhong L 2; Wang CY 1; Yao YG 1,5; Bandelt HJ*6; bandelt@math.uni-hamburg.de
	2008
发表期刊	PLOS ONE
卷号	3 期号:8 页码:e3016
合作性质	其它
摘要	BACKGROUND: 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 imminent 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS: 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.
资助者	The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences. ; The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences. ; The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences. ; The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences.
收录类别	SCI
语种	英语
资助者	The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences. ; The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences. ; The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences. ; The work was supported by grants from National Basic Research Program of China (No. 2007CB507405) and ‘‘Light in Western China’’ of the Chinese Academy of Sciences (to Q-PK). Y-GY was supported by the Chinese Academy of Sciences.
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/6338
专题	科研部门_分子人类学（孔庆鹏）科研部门_动物模型与人类重大疾病机理重点实验室遗传资源与进化国家重点实验室科研部门_疾病机理遗传学和进化医学学科组（姚永刚）
通讯作者	bandelt@math.uni-hamburg.de
作者单位	1.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China 2.Yunnan Univ, Laboratory for Conservat & Utilizat Bio Resource, Kunming, Peoples R China 3.Univ Santiago Compostela, Fac Med, Inst Med Legal, Unidade Xenet, Galicia, Spain 4.Tokyo Metropolitan Inst Gerontol, Dept Genom Longevity & Hlth, Tokyo, Japan 5.Chinese Acad Sci, Kunming Inst Zool, Key Lab Anim Models & Human Dis Mechanisms, Beijing 100864, Peoples R China 6.Univ Hamburg, Dept Math, Hamburg, Germany
推荐引用方式 GB/T 7714	Kong QP,Salas A,Sun C,et al. Distilling artificial recombinants from large sets of complete mtDNA genomes[J]. PLOS ONE,2008,3(8):e3016.
APA	Kong QP.,Salas A.,Sun C.,Fuku N.,Tanaka M.,...&bandelt@math.uni-hamburg.de.(2008).Distilling artificial recombinants from large sets of complete mtDNA genomes.PLOS ONE,3(8),e3016.
MLA	Kong QP,et al."Distilling artificial recombinants from large sets of complete mtDNA genomes".PLOS ONE 3.8(2008):e3016.

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