Distilling artificial recombinants from large sets of complete mtDNA genomes.

PloS One
Qing-Peng KongHans-Jürgen Bandelt

Abstract

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. 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 seq...Continue Reading

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Citations

Sep 4, 2012·International Journal of Legal Medicine·Hans-Jürgen BandeltAntonio Salas
Jul 13, 2011·PloS One·Min-Sheng Peng, Ya-Ping Zhang
Dec 18, 2013·BMC Genomics·Elizabeth A LyonsRebecca S Just
Jun 2, 2010·Molecular Biology and Evolution·Min-Sheng PengYa-Ping Zhang
Nov 3, 2010·Molecular Biology and Evolution·Chiara BatiniDavid Comas
Dec 2, 2011·Molecular Biology and Evolution·Jia LiuQing-Peng Kong
Mar 23, 2012·Journal of Human Genetics·Hua-Wei WangYa-Ping Zhang
Jun 17, 2010·Journal of Cancer Research and Clinical Oncology·Lijun ShenYidong Bai
Dec 4, 2009·Proceedings of the National Academy of Sciences of the United States of America·Mian ZhaoYa-Ping Zhang
Jul 31, 2012·Forensic Science International. Genetics·Antonio SalasWalther Parson
Apr 12, 2011·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Hua-Wei WangYa-Ping Zhang
Jul 1, 2009·Mitochondrion·Hitomi UenoMasashi Tanaka
Oct 29, 2009·Electrophoresis·María CerezoAntonio Salas
Oct 21, 2010·Human Mutation·Anita Kloss-BrandstätterFlorian Kronenberg
Oct 9, 2014·Molecular Ecology·Ni-Ni ShiYa-Ping Zhang
Nov 13, 2015·Scientific Reports·Alberto Gómez-CarballaAntonio Salas
Apr 17, 2016·Nucleic Acids Research·Hansi WeissensteinerSebastian Schönherr
Mar 19, 2014·Forensic Science International. Genetics·Rebecca S JustJodi A Irwin
Dec 17, 2009·American Journal of Human Genetics·Yong-Gang YaoHans-Jürgen Bandelt
Jan 14, 2017·Forensic Science International. Genetics·Tanja HeinzAntonio Salas
May 22, 2019·Molecular Biology and Evolution·Yu-Chun LiQing-Peng Kong
Jun 9, 2009·American Journal of Human Genetics·Pedro SoaresMartin B Richards

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Datasets Mentioned

BETA
EF657790

Methods Mentioned

BETA
PCR
chip

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