RT Journal Article
SR Electronic
T1 Using MinION nanopore sequencing to generate a <em>de novo</em> eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga <em>Galdieria sulphuraria</em> strain SAG 107.79
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 076208
DO 10.1101/076208
A1 Amanda M. Davis
A1 Manuela Iovinella
A1 Sally James
A1 Thomas Robshaw
A1 Jennifer R. Dodson
A1 Lorenzo Herrero-Davila
A1 James H. Clark
A1 Maria Agapiou
A1 Simon J. McQueen-Mason
A1 Gabriele Pinto
A1 Claudia Ciniglia
A1 James P. J. Chong
A1 Peter D. Ashton
A1 Seth J. Davis
YR 2016
UL http://biorxiv.org/content/early/2016/09/20/076208.abstract
AB 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.