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Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107.79

Amanda M. Davis, Manuela Iovinella, Sally James, Thomas Robshaw, Jennifer R. Dodson, Lorenzo Herrero-Davila, James H. Clark, Maria Agapiou, Simon J. McQueen-Mason, Gabriele Pinto, Claudia Ciniglia, James P. J. Chong, Peter D. Ashton, View ORCID ProfileSeth J. Davis
doi: https://doi.org/10.1101/076208
Amanda M. Davis
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Manuela Iovinella
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Sally James
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Thomas Robshaw
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Jennifer R. Dodson
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Lorenzo Herrero-Davila
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James H. Clark
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Maria Agapiou
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Simon J. McQueen-Mason
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Gabriele Pinto
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Claudia Ciniglia
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James P. J. Chong
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Peter D. Ashton
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Seth J. Davis
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  • ORCID record for Seth J. Davis
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Abstract

We report here the de novo assembly of a eukaryotic genome using only MinION nanopore DNA sequence data by examining a novel Galdieria sulphuraria genome: strain SAG 107.79. This extremophilic red alga was targeted for full genome sequencing as we found that it could grow on a wide variety of carbon sources and could uptake several precious and rare-earth metals, which places it as an interesting biological target for disparate industrial biotechnological uses. Phylogenetic analysis clearly places this as a species of G. sulphuraria. Here we additionally show that the genome assembly generated via nanopore long read data was of a high quality with regards to low total number of contiguous DNA sequences and long length of assemblies. Collectively, the MinION platform looks to rival other competing approaches for de novo genome acquisition with available informatics tools for assembly. The genome assembly is publically released as NCBI BioProject PRJNA330791. Further work is needed to reduce small insertion-deletion errors, relative to short-read assemblies.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 20, 2016.
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Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107.79
Amanda M. Davis, Manuela Iovinella, Sally James, Thomas Robshaw, Jennifer R. Dodson, Lorenzo Herrero-Davila, James H. Clark, Maria Agapiou, Simon J. McQueen-Mason, Gabriele Pinto, Claudia Ciniglia, James P. J. Chong, Peter D. Ashton, Seth J. Davis
bioRxiv 076208; doi: https://doi.org/10.1101/076208
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Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107.79
Amanda M. Davis, Manuela Iovinella, Sally James, Thomas Robshaw, Jennifer R. Dodson, Lorenzo Herrero-Davila, James H. Clark, Maria Agapiou, Simon J. McQueen-Mason, Gabriele Pinto, Claudia Ciniglia, James P. J. Chong, Peter D. Ashton, Seth J. Davis
bioRxiv 076208; doi: https://doi.org/10.1101/076208

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