Distilling artificial recombinants from large sets of complete mtDNA genomes.

<h4>Background</h4>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 mar...

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Autores principales:	Qing-Peng Kong, Antonio Salas, Chang Sun, Noriyuki Fuku, Masashi Tanaka, Li Zhong, Cheng-Ye Wang, Yong-Gang Yao, Hans-Jürgen Bandelt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9a48c9a5ac5b4bddbb003d2a3738b99a
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spelling	oai:doaj.org-article:9a48c9a5ac5b4bddbb003d2a3738b99a2021-11-25T06:11:06ZDistilling artificial recombinants from large sets of complete mtDNA genomes.1932-620310.1371/journal.pone.0003016https://doaj.org/article/9a48c9a5ac5b4bddbb003d2a3738b99a2008-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18714389/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions</h4>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.Qing-Peng KongAntonio SalasChang SunNoriyuki FukuMasashi TanakaLi ZhongCheng-Ye WangYong-Gang YaoHans-Jürgen BandeltPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 8, p e3016 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qing-Peng Kong Antonio Salas Chang Sun Noriyuki Fuku Masashi Tanaka Li Zhong Cheng-Ye Wang Yong-Gang Yao Hans-Jürgen Bandelt Distilling artificial recombinants from large sets of complete mtDNA genomes.
description	<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions</h4>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.
format	article
author	Qing-Peng Kong Antonio Salas Chang Sun Noriyuki Fuku Masashi Tanaka Li Zhong Cheng-Ye Wang Yong-Gang Yao Hans-Jürgen Bandelt
author_facet	Qing-Peng Kong Antonio Salas Chang Sun Noriyuki Fuku Masashi Tanaka Li Zhong Cheng-Ye Wang Yong-Gang Yao Hans-Jürgen Bandelt
author_sort	Qing-Peng Kong
title	Distilling artificial recombinants from large sets of complete mtDNA genomes.
title_short	Distilling artificial recombinants from large sets of complete mtDNA genomes.
title_full	Distilling artificial recombinants from large sets of complete mtDNA genomes.
title_fullStr	Distilling artificial recombinants from large sets of complete mtDNA genomes.
title_full_unstemmed	Distilling artificial recombinants from large sets of complete mtDNA genomes.
title_sort	distilling artificial recombinants from large sets of complete mtdna genomes.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/9a48c9a5ac5b4bddbb003d2a3738b99a
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Distilling artificial recombinants from large sets of complete mtDNA genomes.

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