期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 22, 期 4, 页码 -出版社
MDPI
DOI: 10.3390/ijms22041811
关键词
Schistosoma haematobium; mitochondrial (mt) genome; tandem-repetitive DNA; non-coding (control) region; Oxford Nanopore technology; informatics
资金
- Australian Research Council (ARC) [LP180101334, LP180101085]
- National Health and Medical Research Council (NHMRC) of Australia
- ARC Linkage Infrastructure, Equipment and Facilities (LIEF) [LE170100200]
This study demonstrates how third-generation long-read sequencing and informatic methods can accurately characterize long non-coding, tandem-repetitive regions in mitochondrial genomes, overcoming challenges faced by conventional sequencing methods. The discovery of a large tandem-repetitive non-coding region in a metazoan organism raises questions about the evolution and function of potential control regions in mt genomes, prompting further exploration using Nanopore-informatic workflows.
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.
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