RT Journal Article
T1 Distilling Artificial Recombinants from Large Sets of Complete mtDNA Genomes
A1 Kong, Qing-Peng
A1 Salas Ellacuriaga, Antonio
A1 Sun, Chang
A1 Fuku, Noriyuki
A1 Tanaka, Masashi
A1 Zhong, Li
A1 Wang, Cheng-Ye
A1 Yao, Yong-Gang
A1 Bandelt, Hans-Jürgen
AB Background: Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and datahandling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a highimmanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of naturalrecombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise toreticulate patterns and should therefore be detectable.Methodology/Principal Findings: We have developed a strategy for comparing new complete mtDNA genomes, one byone, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from aputative 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 thevariation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with therecombinant 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 severalrecombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novoexperiments – fully concordant with the predictions from our data-analytical approach.
PB PLOS
YR 2008
FD 2008
LK http://hdl.handle.net/10347/22888
UL http://hdl.handle.net/10347/22888
LA eng
NO Kong Q-P, Salas A, Sun C, Fuku N, Tanaka M, Zhong L, et al. (2008) Distilling Artificial Recombinants from Large Sets of Complete mtDNA Genomes. PLoS ONE 3(8): e3016. https://doi.org/10.1371/journal.pone.0003016
NO 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
DS Minerva
RD 24 abr 2026