Roger AJ, Muñoz-Gómez SA, Kamikawa R. The origin and diversification of mitochondria. Curr Biol CB. 2017;27:R1177–92.
Article
CAS
PubMed
Google Scholar
Gray MW. Mitochondrial evolution. Cold Spring Harb Perspect Biol. 2012;4:a011403.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nass MM, Nass S. Intramitochondrial fibers with DNA characteristics. I. Fixation and electron staining reactions. J Cell Biol. 1963;19:593–611.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smith DR. The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs? Brief Funct Genomics. 2016;15:47–54.
CAS
PubMed
Google Scholar
Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC. MITOMAP: a human mitochondrial genome database. Nucleic Acids Res. 1996;24:177–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bernt M, Braband A, Schierwater B, Stadler PF. Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol. 2013;69:328–38.
Article
CAS
PubMed
Google Scholar
Ballard JWO, Whitlock MC. The incomplete natural history of mitochondria. Mol Ecol. 2004;13:729–44.
Article
PubMed
Google Scholar
Allio R, Donega S, Galtier N, Nabholz B. Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker. Mol Biol Evol. 2017;34:2762–72.
Article
CAS
PubMed
Google Scholar
Ramos A, Santos C, Mateiu L, del M Gonzalez M, Alvarez L, Azevedo L, et al. Frequency and pattern of heteroplasmy in the complete human mitochondrial genome. PLoS One. 2013;8:e74636.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pamilo P, Viljakainen L, Vihavainen A. Exceptionally high density of NUMTs in the honeybee genome. Mol Biol Evol. 2007;24:1340–6.
Article
CAS
PubMed
Google Scholar
Ricchetti M, Tekaia F, Dujon B. Continued colonization of the human genome by mitochondrial DNA. PLoS Biol. 2004;2:E273.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nergadze SG, Lupotto M, Pellanda P, Santagostino M, Vitelli V, Giulotto E. Mitochondrial DNA insertions in the nuclear horse genome. Anim Genet. 2010;41(Suppl 2):176–85.
Article
CAS
PubMed
Google Scholar
Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res. 2014;42:12640–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robin ED, Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol. 1988;136:507–13.
Article
CAS
PubMed
Google Scholar
Bensasson D, Zhang D-X, Hartl DL, Hewitt GM. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol. 2001;16:314–21.
Article
CAS
PubMed
Google Scholar
Nguyen TTT, Murphy NP, Austin CM. Amplification of multiple copies of mitochondrial cytochrome b gene fragments in the Australian freshwater crayfish, Cherax destructor Clark (Parastacidae: Decapoda). Anim Genet. 2002;33:304–8.
Article
CAS
PubMed
Google Scholar
Yao Y-G, Kong Q-P, Salas A, Bandelt H-J. Pseudomitochondrial genome haunts disease studies. J Med Genet. 2008;45:769–72.
Article
CAS
PubMed
Google Scholar
Maddock ST, Briscoe AG, Wilkinson M, Waeschenbach A, Mauro DS, Day JJ, et al. Next-generation mitogenomics: a comparison of approaches applied to caecilian amphibian phylogeny. PLoS One. 2016;11:e0156757.
Article
PubMed
PubMed Central
CAS
Google Scholar
Briscoe AG, Hopkins KP, Waeschenbach A. High-throughput sequencing of complete mitochondrial genomes. Methods Mol Biol Clifton NJ. 2016;1452:45–64.
Article
CAS
Google Scholar
Istace B, Friedrich A, d’Agata L, Faye S, Payen E, Beluche O, et al. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience. 2017;6. https://doi.org/10.1093/gigascience/giw018.
Ranjard L, Wong TKF, Külheim C, Rodrigo AG, Ragg NLC, Patel S, et al. Complete mitochondrial genome of the green-lipped mussel, Perna canaliculus (Mollusca: Mytiloidea), from long nanopore sequencing reads. Mitochondrial DNA Part B. 2018;3:175–6.
Article
Google Scholar
Gan HM, Grandjean F, Jenkins TL, Austin CM. Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication. BMC Genomics. 2019;20:335.
Article
PubMed
PubMed Central
Google Scholar
Gan HM, Linton SM, Austin CM. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes. Mar Genomics. 2019;45:64–71.
Article
PubMed
Google Scholar
Barrey E, Mucher E, Jeansoule N, Larcher T, Guigand L, Herszberg B, et al. Gene expression profiling in equine polysaccharide storage myopathy revealed inflammation, glycogenesis inhibition, hypoxia and mitochondrial dysfunctions. BMC Vet Res. 2009;5:29.
Article
PubMed
PubMed Central
CAS
Google Scholar
Barrey E, Jayr L, Mucher E, Gospodnetic S, Joly F, Benech P, et al. Transcriptome analysis of muscle in horses suffering from recurrent exertional rhabdomyolysis revealed energetic pathway alterations and disruption in the cytosolic calcium regulation. Anim Genet. 2012;43:271–81.
Article
CAS
PubMed
Google Scholar
Mach N, Plancade S, Pacholewska A, Lecardonnel J, Rivière J, Moroldo M, et al. Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse. Sci Rep. 2016;6:22932.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ricard A, Robert C, Blouin C, Baste F, Torquet G, Morgenthaler C, et al. Endurance exercise ability in the horse: a trait with complex polygenic determinism. Front Genet. 2017;8:89.
Article
PubMed
PubMed Central
CAS
Google Scholar
Keyser-Tracqui C, Blandin-Frappin P, Francfort H-P, Ricaut F-X, Lepetz S, Crubézy E, et al. Mitochondrial DNA analysis of horses recovered from a frozen tomb (Berel site, Kazakhstan, 3rd century BC). Anim Genet. 2005;36:203–9.
Article
CAS
PubMed
Google Scholar
Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, et al. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc Natl Acad Sci U S A. 2012;109:2449–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, et al. Tracking five millennia of horse management with extensive ancient genome time series. Cell. 2019;177:1419–1435.e31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolff JN, Shearman DCA, Brooks RC, Ballard JWO. Selective enrichment and sequencing of whole mitochondrial genomes in the presence of nuclear encoded mitochondrial pseudogenes (numts). PLoS One. 2012;7:e37142.
Article
CAS
PubMed
PubMed Central
Google Scholar
Santibanez-Koref M, Griffin H, Turnbull DM, Chinnery PF, Herbert M, Hudson G. Assessing mitochondrial heteroplasmy using next generation sequencing: a note of caution. Mitochondrion. 2019;46:302–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jayaprakash AD, Benson EK, Gone S, Liang R, Shim J, Lambertini L, et al. Stable heteroplasmy at the single-cell level is facilitated by intercellular exchange of mtDNA. Nucleic Acids Res. 2015;43:2177–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marquis J, Lefebvre G, Kourmpetis YAI, Kassam M, Ronga F, De Marchi U, et al. MitoRS, a method for high throughput, sensitive, and accurate detection of mitochondrial DNA heteroplasmy. BMC Genomics. 2017;18. https://doi.org/10.1186/s12864-017-3695-5.
Huszar TI, Wetton JH, Jobling MA. Mitigating the effects of reference sequence bias in single-multiplex massively parallel sequencing of the mitochondrial DNA control region. Forensic Sci Int Genet. 2019;40:9–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fazzini F, Schöpf B, Blatzer M, Coassin S, Hicks AA, Kronenberg F, et al. Plasmid-normalized quantification of relative mitochondrial DNA copy number. Sci Rep. 2018;8:15347.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hutchison CA, Smith HO, Pfannkoch C, Venter JC. Cell-free cloning using φ29 DNA polymerase. Proc Natl Acad Sci U S A. 2005;102:17332–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ellegaard KM, Klasson L, Andersson SGE. Testing the reproducibility of multiple displacement amplification on genomes of clonal Endosymbiont populations. PLoS One. 2013;8:e82319.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tu J, Guo J, Li J, Gao S, Yao B, Lu Z. Systematic characteristic exploration of the chimeras generated in multiple displacement amplification through next generation sequencing data reanalysis. PLoS One. 2015;10. https://doi.org/10.1371/journal.pone.0139857.
Quispe-Tintaya W, White RR, Popov VN, Vijg J, Maslov AY. Fast mitochondrial DNA isolation from mammalian cells for next-generation sequencing. BioTechniques. 2013;55:133–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simison WB, Lindberg DR, Boore JL. Rolling circle amplification of metazoan mitochondrial genomes. Mol Phylogenet Evol. 2006;39:562–7.
Article
CAS
PubMed
Google Scholar
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: comparison of ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics. 2012;13:341.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lanave C, Tommasi S, Preparata G, Saccone C. Transition and transversion rate in the evolution of animal mitochondrial DNA. Biosystems. 1986;19:273–83.
Article
CAS
PubMed
Google Scholar
Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, et al. The diversity present in 5140 human mitochondrial genomes. Am J Hum Genet. 2009;84:628–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stoltzfus A, Norris RW. On the causes of evolutionary transition: transversion bias. Mol Biol Evol. 2016;33:595–602.
Article
CAS
PubMed
Google Scholar
Guo Y, Ye F, Sheng Q, Clark T, Samuels DC. Three-stage quality control strategies for DNA re-sequencing data. Brief Bioinform. 2014;15:879–89.
Article
CAS
PubMed
Google Scholar
Edge P, Bansal V. Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing. Nat Commun. 2019;10:4660.
Article
PubMed
PubMed Central
CAS
Google Scholar
Luo R, Sedlazeck FJ, Lam T-W, Schatz MC. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019;10:998.
Article
PubMed
PubMed Central
CAS
Google Scholar
Casane D, Dennebouy N, de Rochambeau H, Mounolou JC, Monnerot M. Nonneutral evolution of tandem repeats in the mitochondrial DNA control region of lagomorphs. Mol Biol Evol. 1997;14:779–89.
Article
CAS
PubMed
Google Scholar
White EJ, Ross T, Lopez E, Nikiforov A, Gault C, Batorsky R, et al. Chasing a moving target: Detection of mitochondrial heteroplasmy for clinical diagnostics. bioRxiv. 2017:222109.
Tan AS, Baty JW, Dong L-F, Bezawork-Geleta A, Endaya B, Goodwin J, et al. Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab. 2015;21:81–94.
Article
CAS
PubMed
Google Scholar
Lindberg MR, Schmedes SE, Hewitt FC, Haas JL, Ternus KL, Kadavy DR, et al. A comparison and integration of MiSeq and MinION platforms for sequencing single source and mixed mitochondrial genomes. PLoS One. 2016;11:e0167600.
Article
PubMed
PubMed Central
CAS
Google Scholar
Castro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins KH, McIntyre ABR, et al. Nanopore DNA sequencing and genome assembly on the international Space Station. Sci Rep. 2017;7:1–12.
Article
CAS
Google Scholar
Zascavage RR, Thorson K, Planz JV. Nanopore sequencing: an enrichment-free alternative to mitochondrial DNA sequencing. Electrophoresis. 2019;40:272–80.
Article
CAS
PubMed
Google Scholar
Loose M, Malla S, Stout M. Real-time selective sequencing using nanopore technology. Nat Methods. 2016;13:751–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Noakes MT, Brinkerhoff H, Laszlo AH, Derrington IM, Langford KW, Mount JW, et al. Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage. Nat Biotechnol. 2019;37:651–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rang FJ, Kloosterman WP, de Ridder J. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol. 2018;19:90.
Article
PubMed
PubMed Central
CAS
Google Scholar
McNaughton AL, Roberts HE, Bonsall D, de Cesare M, Mokaya J, Lumley SF, et al. Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV). Sci Rep. 2019;9:1–14.
Article
CAS
Google Scholar
Robert C, Valette J-P, Jacquet S, Lepeule J, Denoix J-M. Study design for the investigation of likely aetiological factors of juvenile osteochondral conditions (JOCC) in foals and yearlings. Vet J Lond Engl 1997. 2013;197:36–43.
Google Scholar
Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, Geigl E-M. An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One. 2010;5.
De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34:2666–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinforma Oxf Engl. 2018;34:3094–100.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinforma Oxf Engl. 2009;25:2078–9.
Article
CAS
Google Scholar
Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2009. https://doi.org/10.1007/978-0-387-98141-3.
Book
Google Scholar
R Core Team. R: A language and environment for statistical computing. 2019. www.R-project.org.
Google Scholar