Fidelity of DNA Polymerases in the Detection of Intraindividual Variation of Mitochondrial DNA

Overview

Journal Mitochondrial DNA B Resour

Date 2020 Dec 28

PMID 33366444

Citations 6

Authors

Paulo Cseri Ricardo

Elaine Francoso

Maria Cristina Arias

Affiliations

Soon will be listed here.

Abstract

Here we investigated the consequences of PCR amplification errors in the identification of intraindividual mtDNA variation. The bumblebee was chosen as model for the gene amplification tests with two DNA polymerases ( and Q5) presenting different error rates. The amplifications using resulted in a significant increase of singleton haplotypes per individual in comparison to Q5. The sequence characteristics indicated that 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.

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References

McInerney P, Adams P, Hadi M . Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase. Mol Biol Int. 2014; 2014:287430. PMC: 4150459. DOI: 10.1155/2014/287430. View

Smith J, Modrich P . Removal of polymerase-produced mutant sequences from PCR products. Proc Natl Acad Sci U S A. 1997; 94(13):6847-50. PMC: 21247. DOI: 10.1073/pnas.94.13.6847. View

Keohavong P, Thilly W . Fidelity of DNA polymerases in DNA amplification. Proc Natl Acad Sci U S A. 1989; 86(23):9253-7. PMC: 298472. DOI: 10.1073/pnas.86.23.9253. View

Yamagami T, Ishino S, Kawarabayasi Y, Ishino Y . Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering. Front Microbiol. 2014; 5:461. PMC: 4153296. DOI: 10.3389/fmicb.2014.00461. View

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S . Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12):1647-9. PMC: 3371832. DOI: 10.1093/bioinformatics/bts199. View

Richly E, Leister D . NUMTs in sequenced eukaryotic genomes. Mol Biol Evol. 2004; 21(6):1081-4. DOI: 10.1093/molbev/msh110. View

Reiss J, Krawczak M, Schloesser M, Wagner M, Cooper D . The effect of replication errors on the mismatch analysis of PCR-amplified DNA. Nucleic Acids Res. 1990; 18(4):973-8. PMC: 330352. DOI: 10.1093/nar/18.4.973. View

Paradis E . pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics. 2010; 26(3):419-20. DOI: 10.1093/bioinformatics/btp696. View

Cline J, Braman J, Hogrefe H . PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 1996; 24(18):3546-51. PMC: 146123. DOI: 10.1093/nar/24.18.3546. View

10.

Pascual V, Liu Y, Magalski A, de Bouteiller O, Banchereau J, Capra J . Analysis of somatic mutation in five B cell subsets of human tonsil. J Exp Med. 1994; 180(1):329-39. PMC: 2191579. DOI: 10.1084/jem.180.1.329. View

11.

Bandelt H, Forster P, Rohl A . Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16(1):37-48. DOI: 10.1093/oxfordjournals.molbev.a026036. View

12.

ECKERT K, Kunkel T . High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. Nucleic Acids Res. 1990; 18(13):3739-44. PMC: 331072. DOI: 10.1093/nar/18.13.3739. View

13.

Lin M, Simon D, Ahn C, Kim L, Beal M . High aggregate burden of somatic mtDNA point mutations in aging and Alzheimer's disease brain. Hum Mol Genet. 2002; 11(2):133-45. DOI: 10.1093/hmg/11.2.133. View

14.

Francoso E, Gomes F, Arias M . A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2015; 27(4):2401-4. DOI: 10.3109/19401736.2015.1028049. View

15.

Librado P, Rozas J . DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25(11):1451-2. DOI: 10.1093/bioinformatics/btp187. View

16.

Li M, Diehl F, Dressman D, Vogelstein B, Kinzler K . BEAMing up for detection and quantification of rare sequence variants. Nat Methods. 2006; 3(2):95-7. DOI: 10.1038/nmeth850. View

17.

Saiki R, Gelfand D, Stoffel S, Scharf S, Higuchi R, Horn G . Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988; 239(4839):487-91. DOI: 10.1126/science.2448875. View

18.

Francoso E, Zuntini A, Carnaval A, Arias M . Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees. BMC Evol Biol. 2016; 16(1):267. PMC: 5142330. DOI: 10.1186/s12862-016-0803-0. View

19.

Kunkel T, Bebenek K . DNA replication fidelity. Annu Rev Biochem. 2000; 69:497-529. DOI: 10.1146/annurev.biochem.69.1.497. View

20.

Bracho M, Moya A, Barrio E . Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol. 1999; 79 ( Pt 12):2921-8. DOI: 10.1099/0022-1317-79-12-2921. View