Chandler, Jodie;
Camberis, Mali;
Bouchery, Tiffany;
Blaxter, Mark;
Le Gros, Graham;
Eccles, David A;
(2017)
Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis.
F1000Research
, 6
, Article 56. 10.12688/f1000research.10545.1.
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Abstract
Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensis using MinION R9 nanopore data. The assembly was error-corrected using existing Illumina HiSeq reads, and annotated in full (i.e. gene boundary definitions without substantial gaps) by comparing with annotated genomes from similar parasite relatives. The mitochondrial genome has also been annotated with a preliminary electrical consensus sequence, using raw signal data generated from a Nanopore R9 flow cell.
| Type: | Article |
|---|---|
| Title: | Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.12688/f1000research.10545.1 |
| Publisher version: | https://doi.org/10.12688/f1000research.10545.1 |
| Language: | English |
| Additional information: | © 2017 Chandler J et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | Nanopore, MinION, parasite, mitochondria, de novo, phylogenetic, bioinformatics |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10189156 |
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