Fidelity of DNA polymerases in the detection of intraindividual variation of mitochondrial DNA

Abstract Here we investigated the consequences of PCR amplification errors in the identification of intraindividual mtDNA variation. The bumblebee Bombus morio was chosen as model for the COI gene amplification tests with two DNA polymerases (Taq and Q5) presenting different error rates. The amplifications using Taq resulted in a significant increase of singleton haplotypes per individual in comparison to Q5. The sequence characteristics indicated that Taq resulted haplotypes are mostly due to amplification errors. Studies focusing on intraindividual variability should address special attention to the DNA polymerase fidelity to avoid overestimation of heteroplasmic haplotypes.

[1]  Vladimir Potapov,et al.  Examining Sources of Error in PCR by Single-Molecule Sequencing , 2017, PloS one.

[2]  M. C. Arias,et al.  Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees , 2016, BMC Evolutionary Biology.

[3]  M. C. Arias,et al.  A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae) , 2016, Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.

[4]  David Bryant,et al.  popart: full‐feature software for haplotype network construction , 2015 .

[5]  Y. Kawarabayasi,et al.  Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering , 2014, Front. Microbiol..

[6]  Masood Z. Hadi,et al.  Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase , 2014, Molecular biology international.

[7]  M. C. Arias,et al.  Cytochrome c oxidase I primers for corbiculate bees: DNA barcode and mini‐barcode , 2013, Molecular ecology resources.

[8]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[9]  E. Paradis.  pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[10]  Pablo Librado,et al.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data , 2009, Bioinform..

[11]  Frank Diehl,et al.  BEAMing up for detection and quantification of rare sequence variants , 2006, Nature Methods.

[12]  Dario Leister,et al.  NUMTs in sequenced eukaryotic genomes. , 2004, Molecular biology and evolution.

[13]  T. Kunkel.  DNA Replication Fidelity* , 2004, Journal of Biological Chemistry.

[14]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[15]  M. Beal,et al.  High aggregate burden of somatic mtDNA point mutations in aging and Alzheimer's disease brain. , 2002, Human molecular genetics.

[16]  A. Moya,et al.  Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. , 1998, The Journal of general virology.

[17]  P. Modrich,et al.  Removal of polymerase-produced mutant sequences from PCR products. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[18]  J. Braman,et al.  PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. , 1996, Nucleic acids research.

[19]  B. Crespi,et al.  Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers , 1994 .

[20]  V. Pascual,et al.  Analysis of somatic mutation in five B cell subsets of human tonsil , 1994, The Journal of experimental medicine.

[21]  K. A. Eckert,et al.  High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase , 1990, Nucleic Acids Res..

[22]  P. Parham,et al.  Rapid cloning of HLA-A,B cDNA by using the polymerase chain reaction: frequency and nature of errors produced in amplification. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[23]  M Krawczak,et al.  The effect of replication errors on the mismatch analysis of PCR-amplified DNA. , 1990, Nucleic acids research.

[24]  W. Thilly,et al.  Fidelity of DNA polymerases in DNA amplification. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[25]  S E Humphries,et al.  Errors in the polymerase chain reaction. , 1988, Nucleic acids research.

[26]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[27]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[28]  T. Kunkel.  DNA replication fidelity. , 2004, The Journal of biological chemistry.

[29]  H. Bandelt,et al.  Median-joining networks for inferring intraspecific phylogenies. , 1999, Molecular biology and evolution.

[30]  T. Kunkel,et al.  DNA replication fidelity. , 1992, The Journal of biological chemistry.