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Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis.

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.

SUBMITTER: Chandler J

PROVIDER: S-EPMC5399971 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis.

Chandler Jodie J Camberis Mali M Bouchery Tiffany T Blaxter Mark M Le Gros Graham G Eccles David A DA

F1000Research 20170119

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 mitochondri ...[more]

PMID: 28491281

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