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Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 30, 2019 - Issue 8
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Research Articles

Portunus pelagicus mtDNA heteroplasmy inheritance and its effect on the use of mtCR and mtCOI sequence data

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Pages 848-860 | Received 09 Jul 2019, Accepted 10 Nov 2019, Published online: 25 Nov 2019

References

  • Abascal F, Zardoya R, Telford MJ. 2010. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38(Suppl. 2):W7–W13.
  • Alacs EA, Georges A, FitzSimmons NN, Robertson J. 2009. DNA detective: a review of molecular approaches to wildlife forensics. Forensic Sci Med Pathol. 6:180–194.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410.
  • Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Cambridge, UK: Abraham Institute. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477.
  • Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. 2011. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 27(12):1691–1692.
  • Bernt M, Braband A, Schierwater B, Stadler PF. 2013. Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol. 69(2):328–338.
  • Bhatti S, Aslam Khan M, Abbas S, Attimonelli M, Gonzalez GR, Aydin HH, de Souza E. 2018. Problems in mitochondrial DNA forensics: while interpreting length heteroplasmy conundrum of various Sindhi and Baluchi ethnic groups of Pakistan. Mitochondrial DNA A. 29(4):501–510.
  • Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, Taylor J, Nekrutenko A. 2014. Dissemination of scientific software with Galaxy ToolShed. Genome Biol. 15(2):403.
  • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
  • Breton S, Beaupre HD, Stewart DT, Hoeh WR, Blier PU. 2007. The unusual system of doubly uniparental inheritance of mtDNA: isn’t one enough? Trends Genet. 23(9):465–474.
  • Brown WM, George M, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA. 76(4):1967.
  • Burr SP, Pezet M, Chinnery PF. 2018. Mitochondrial DNA heteroplasmy and purifying selection in the mammalian female germ line. Dev Growth Differ. 60(1):21–32.
  • Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA and human evolution. Nature. 325(6099):31–36.
  • Chinnery PF, Howell N, Lightowlers RN, Turnbull DM. 1997. Molecular pathology of MELAS and MERRF. The relationship between mutation load and clinical phenotypes. Brain. 120(10):1713–1721.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772.
  • Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, et al. 2018. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One. 13(2):e0192567.
  • Dierckxsens N, Mardulyn P, Smits G. 2016. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45:e18.
  • Duan M, Tu J, Lu Z. 2018. Recent advances in detecting mitochondrial DNA heteroplasmic variations. Molecules. 23:323.
  • Ekblom R, Smeds L, Ellegren H. 2014. Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. BMC Genomics. 15(1):467.
  • Fan W, Waymire KG, Narula N, Li P, Rocher C, Coskun PE, Vannan MA, Narula J, MacGregor GR, Wallace DC. 2008. A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations. Science. 319(5865):958.
  • Floros VI, Pyle A, Dietmann S, Wei W, Tang WCW, Irie N, Payne B, Capalbo A, Noli L, Coxhead J, et al. 2018. Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos. Nat Cell Biol. 20(2):144–151.
  • Garrison E, Marth G. 2012. Haplotype-based variant detection from short-read sequencing. arXiv Preprint arXiv:12073907.
  • Goecks J, Nekrutenko A, Taylor J. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11(8):R86.
  • Greaves LC, Nooteboom M, Elson JL, Tuppen HAL, Taylor GA, Commane DM, Arasaradnam RP, Khrapko K, Taylor RW, Kirkwood TBL, et al. 2014. Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing. PLoS Genet. 10(9):e1004620.
  • Guo E, Liu Y, Cui Z, Li X, Cheng Y, Wu X. 2012. Genetic variation and population structure of swimming crab (Portunus trituberculatus) inferred from mitochondrial control region. Mol Biol Rep. 39(2):1453–1463.
  • Guo Y, Li C-I, Sheng Q, Winther JF, Cai Q, Boice JD, Shyr Y. 2013. Very low-level heteroplasmy mtDNA variations are inherited in humans. J Genet Genomics. 40(12):607–615.
  • Guo Y, Li J, Li C-I, Long J, Samuels DC, Shyr Y. 2012. The effect of strand bias in Illumina short-read sequencing data. BMC Genomics. 13(1):666.
  • Hill JT, Demarest BL, Bisgrove BW, Su YC, Smith M, Yost HJ. 2014. Poly peak parser: method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products. Dev Dyn. 243(12):1632–1636.
  • Ingman M, Kaessmann H, Pääbo S, Gyllensten U. 2000. Mitochondrial genome variation and the origin of modern humans. Nature. 408(6813):708.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
  • Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874.
  • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 25(14):1754–1760.
  • Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 26(5):589–595.
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics. 25(16):2078–2079.
  • Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv Preprint arXiv:13033997.
  • Li M, Rothwell R, Vermaat M, Wachsmuth M, Schröder R, Laros JFJ, van Oven M, de Bakker PIW, Bovenberg JA, van Duijn CM, et al. 2016. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck. Genome Res. 26(4):417–426.
  • Luo A, Zhang A, Ho SYW, Xu W, Zhang Y, Shi W, Cameron SL, Zhu C. 2011. Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. BMC Genomics. 12(1):84.
  • Ma H, Xu H, O'Farrell PH. 2014. Transmission of mitochondrial mutations and action of purifying selection in Drosophila melanogaster. Nat Genet. 46(4):393.
  • Magnacca KN, Brown MJ. 2010. Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae). BMC Evol Biol. 10(1):174.
  • Maitra A, Cohen Y, Gillespie SE, Mambo E, Fukushima N, Hoque MO, Shah N, Goggins M, Califano J, Sidransky D. 2004. The human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res. 14(5):812–819.
  • Manjunath BC, Chandrashekar BR, Mahesh M, Vatchala Rani RM. 2011. DNA profiling and forensic dentistry – a review of the recent concepts and trends. J Forensic Leg Med. 18(5):191–197.
  • Meng X-L, Jia F-L, Liu P, Li J. 2016. The complete mitogenome of blue swimming crab Portunus pelagicus Linnaeus, 1766 (Crustacea: Decapoda: Portunidae). Mitochondrial DNA A. 27:2789–2790.
  • Merheb M, Matar R, Hodeify R, Siddiqui SS, Vazhappilly CG, Marton J, Azharuddin S, Al Zouabi H. 2019. Mitochondrial DNA, a powerful tool to decipher ancient human civilization from domestication to music, and to uncover historical murder cases. Cells. 8(5):433.
  • Ortman BD, Bucklin A, Pagès F, Youngbluth M. 2010. DNA barcoding the Medusozoa using mtCOI. Deep Sea Res II Top Stud Oceanogr. 57(24–26):2148–2156.
  • Otten ABC, Sallevelt S, Carling PJ, Dreesen J, Drüsedau M, Spierts S, Paulussen ADC, de Die-Smulders CEM, Herbert M, Chinnery PF, et al. 2018. Mutation-specific effects in germline transmission of pathogenic mtDNA variants. Hum Reprod. 33(7):1331–1341.
  • Payne BA, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF. 2013. Universal heteroplasmy of human mitochondrial DNA. Hum Mol Genet. 22(2):384–390.
  • Rambaut A. 2012. FigTree v1. 4. Molecular evolution, phylogenetics and epidemiology. Edinburgh: University of Edinburgh, Institute of Evolutionary Biology.
  • Rebolledo-Jaramillo B, Su MS-W, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, et al. 2014. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc Natl Acad Sci USA. 111(43):15474–15479.
  • Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61(3):539–542.
  • Samehsalari S, Reddy KR. 2018. Application control region of human mitochondrial DNA in forensic anthropology. Int J Mod Anthrop. 2(11):233–248.
  • Sharpley Mark S, Marciniak C, Eckel-Mahan K, McManus M, Crimi M, Waymire K, Lin Chun S, Masubuchi S, Friend N, Koike M, et al. 2012. Heteroplasmy of mouse mtDNA is genetically unstable and results in altered behavior and cognition. Cell. 151(2):333–343.
  • Silvestro D, Michalak I. 2012. raxmlGUI: a graphical front-end for RAxML. Org Divers Evol. 12:335–337.
  • Stewart JB, Chinnery PF. 2015. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat Rev Genet. 16(9):530.
  • Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson NG. 2008. Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biol. 6(1):e10.
  • Stucky BJ. 2012. SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms. J Biomol Tech. 23(3):90–93.
  • White DJ, Wolff JN, Pierson M, Gemmell NJ. 2008. Revealing the hidden complexities of mtDNA inheritance. Mol Ecol. 17(23):4925–4942.
  • Williams EP, Feng X, Place AR. 2017. Extensive heteroplasmy and evidence for fragmentation in the Callinectes sapidus mitochondrial genome. J Shellfish Res. 36(1):263–273.
  • Wolff JN, White DJ, Woodhams M, White HE, Gemmell NJ. 2011. The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates. PLoS One. 6(5):e20522.
  • Wonnapinij P, Chinnery PF, Samuels DC. 2010. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans. Am J Hum Genet. 86(4):540–550.
  • Xiang H, Gao J, Cai D, Luo Y, Yu B, Liu L, Liu R, Zhou H, Chen X, Dun W, et al. 2017. Origin and dispersal of early domestic pigs in northern China. Sci Rep. 7(1):5602.
  • Xiufeng X, Árnason Ú. 1994. The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region. Gene. 148(2):357–362.

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