Journal article

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

Liina Kinkar, Robin B Gasser, Bonnie L Webster, David Rollinson, D Timothy J Littlewood, Bill CH Chang, Andreas J Stroehlein, Pasi K Korhonen, Neil D Young

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES | MDPI | Published : 2021

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 ..

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Grants

Awarded by Australian Research Council (ARC)


Awarded by ARC Linkage Infrastructure, Equipment and Facilities (LIEF)


Funding Acknowledgements

This project was supported through grants LP180101334 (N.D.Y. and P.K.K.) and LP180101085 (R.B.G. and B.C.H.C.) from the Australian Research Council (ARC). P.K.K. held an Early Career Research Fellowship from the National Health and Medical Research Council (NHMRC) of Australia. We acknowledge the use of HPC-GPGPU Facility computer resources hosted at the University of Melbourne. This Facility is supported by ARC Linkage Infrastructure, Equipment and Facilities (LIEF) Grant LE170100200.