What is it about?
We have assembled a mitochondrial genome of a rodent parasite using reads generated by the MinION long-read sequencer. DNA was extracted with minimal processing and no filtering, and the mitochondrial sequence "fell out" after attempting an assembly of the reads output by the sequencer.
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Why is it important?
This is the beginning of our project to improve the annotation and sequence assembly of the rodent parasite, Nippostrongylus brasiliensis. To help other researchers, we provide a detailed methodology, the mitochondrial sequence, annotated gene boundaries, and a consensus electrical signal generated by the MinION DNA sequencer.
Perspectives
This is my first foray into managing research projects. I helped organise and carry out the sequencing and data analysis for this project. A lot of the data analysis side of this project has been me testing the water to see what is possible with only a few nanopore reads -- there's a lot of information available that tends to be ignored when people only concentrate on the final base-called consensus sequence. Despite that, this is more of a data release paper than a data analysis paper; I didn't want to get too bogged down in the details of analysis and leave behind a huge paper that no one will bother reading. One of the interesting findings of this project was the discovery of heterogeneity within mitochondrial DNA sequences, both in the Wellcome Trust Sanger Institute reads, as well as in our reads at the Malaghan Institute. We found a few variants in both strains that were at frequencies of close to 50%, suggesting a reasonable amount of diversity within maintained strains of this parasite, particularly when considering the low rate of mutation of the mitochondrial genome.
Dr David A Eccles
Malaghan Institute of Medical Research
Read the Original
This page is a summary of: Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis, F1000Research, January 2017, Faculty of 1000, Ltd.,
DOI: 10.12688/f1000research.10545.1.
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