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

Kinkar, Liina
; 
Gasser, Robin
; ; ; ; 
Chang, Bill
; 
Stroehlein, Andreas
; 
Korhonen, Pasi
; 
Young, Neil
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2021-02-11
Submitted Date
2021-01-27
Subject Terms
Schistosoma haematobium
mitochondrial (mt) genome
tandem-repetitive DNA
noncoding (control) region
Oxford Nanopore technology
informatics
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Life sciences
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Abstract
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.
Citation
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
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MDPI AG
Journal
International Journal of Molecular Sciences
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http://hdl.handle.net/10141/622983
DOI
10.3390/ijms22041811
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Journal Article
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Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).
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1422-0067
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1422-0067
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openAccess
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