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Article

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

1
Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
2
Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
3
London Centre for Neglected Tropical Disease Research, London W12 1PG, UK
*
Authors to whom correspondence should be addressed.
Academic Editor: Miroslav Plohl
Int. J. Mol. Sci. 2021, 22(4), 1811; https://doi.org/10.3390/ijms22041811
Received: 27 January 2021 / Accepted: 8 February 2021 / Published: 11 February 2021
(This article belongs to the Special Issue Repetitive DNA Sequences in Eukaryotic Genomes)
Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow. View Full-Text
Keywords: Schistosoma haematobium; mitochondrial (mt) genome; tandem-repetitive DNA; non-coding (control) region; Oxford Nanopore technology; informatics Schistosoma haematobium; mitochondrial (mt) genome; tandem-repetitive DNA; non-coding (control) region; Oxford Nanopore technology; informatics
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MDPI and ACS Style

Kinkar, L.; Gasser, R.B.; Webster, B.L.; Rollinson, D.; Littlewood, D.T.J.; Chang, B.C.H.; Stroehlein, A.J.; Korhonen, P.K.; Young, N.D. Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. Int. J. Mol. Sci. 2021, 22, 1811. https://doi.org/10.3390/ijms22041811

AMA Style

Kinkar L, Gasser RB, Webster BL, Rollinson D, Littlewood DTJ, Chang BCH, Stroehlein AJ, Korhonen PK, Young ND. Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. International Journal of Molecular Sciences. 2021; 22(4):1811. https://doi.org/10.3390/ijms22041811

Chicago/Turabian Style

Kinkar, Liina, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. T.J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, and Neil D. Young 2021. "Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes" International Journal of Molecular Sciences 22, no. 4: 1811. https://doi.org/10.3390/ijms22041811

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