First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach.
Background Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability...
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ftdoajarticles:oai:doaj.org/article:4b4181449fbb46208dd7dd01e40614d2 2023-05-15T15:15:32+02:00 First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. Liina Kinkar Neil D Young Woon-Mok Sohn Andreas J Stroehlein Pasi K Korhonen Robin B Gasser 2020-08-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0008552 https://doaj.org/article/4b4181449fbb46208dd7dd01e40614d2 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0008552 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0008552 https://doaj.org/article/4b4181449fbb46208dd7dd01e40614d2 PLoS Neglected Tropical Diseases, Vol 14, Iss 8, p e0008552 (2020) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2020 ftdoajarticles https://doi.org/10.1371/journal.pntd.0008552 2022-12-31T07:51:21Z Background Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome-including the long, non-coding region-of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing. Methods The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach. Results From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719-809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation. Conclusions For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 14 8 e0008552 |
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English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Liina Kinkar Neil D Young Woon-Mok Sohn Andreas J Stroehlein Pasi K Korhonen Robin B Gasser First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
Background Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome-including the long, non-coding region-of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing. Methods The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach. Results From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719-809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation. Conclusions For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of ... |
format |
Article in Journal/Newspaper |
author |
Liina Kinkar Neil D Young Woon-Mok Sohn Andreas J Stroehlein Pasi K Korhonen Robin B Gasser |
author_facet |
Liina Kinkar Neil D Young Woon-Mok Sohn Andreas J Stroehlein Pasi K Korhonen Robin B Gasser |
author_sort |
Liina Kinkar |
title |
First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. |
title_short |
First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. |
title_full |
First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. |
title_fullStr |
First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. |
title_full_unstemmed |
First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. |
title_sort |
first record of a tandem-repeat region within the mitochondrial genome of clonorchis sinensis using a long-read sequencing approach. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2020 |
url |
https://doi.org/10.1371/journal.pntd.0008552 https://doaj.org/article/4b4181449fbb46208dd7dd01e40614d2 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 14, Iss 8, p e0008552 (2020) |
op_relation |
https://doi.org/10.1371/journal.pntd.0008552 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0008552 https://doaj.org/article/4b4181449fbb46208dd7dd01e40614d2 |
op_doi |
https://doi.org/10.1371/journal.pntd.0008552 |
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PLOS Neglected Tropical Diseases |
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14 |
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8 |
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e0008552 |
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