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Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device

John R Tyson, Nigel J O'Neil, Miten Jain, Hugh E Olsen, Philip Hieter, Terrance P Snutch
doi: https://doi.org/10.1101/099143
John R Tyson
University of British Columbia;
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  • For correspondence: jtyson@msl.ubc.ca
Nigel J O'Neil
University of British Columbia;
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Miten Jain
University of California Santa Cruz
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Hugh E Olsen
University of California Santa Cruz
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Philip Hieter
University of British Columbia;
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Terrance P Snutch
University of British Columbia;
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Abstract

Advances in 3rd generation sequencing have opened new possibilities for benchtop whole genome sequencing. The MinION is a portable device that uses nanopore technology and can sequence long DNA molecules. MinION long reads are well suited for sequencing and de novo assembly of complex genomes with large repetitive elements. Long reads also facilitate the identification of complex genomic rearrangements such as those observed in tumor genomes. To assess the feasibility of the de novo assembly of large complex genomes using both MinION and Illumina platforms, we sequenced the genome of a Caenorhabditis elegans strain that contains a complex acetaldehyde-induced rearrangement and a biolistic bombardment-mediated insertion of a GFP containing plasmid. Using ~5.8 gigabases of MinION sequence data, we were able to assemble a C. elegans genome containing 145 contigs (N50 contig length = 1.22 Mb) that covered >99% of the 100,286,401 bp reference genome. In contrast, using ~8.04 gigabases of Illumina sequence data, we were able to assemble a C. elegans genome in 38,645 contigs (N50 contig length = ~26 kb) containing 117 Mb. From the MinION genome assembly we identified the complex structures of both the acetaldehyde-induced mutation and the biolistic-mediated insertion. To date, this is the largest genome to be assembled exclusively from MinION data and is the first demonstration that the long reads of MinION sequencing can be used for whole genome assembly of large (100 Mb) genomes and the elucidation of complex genomic rearrangements.

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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 January 30, 2017.
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Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device
John R Tyson, Nigel J O'Neil, Miten Jain, Hugh E Olsen, Philip Hieter, Terrance P Snutch
bioRxiv 099143; doi: https://doi.org/10.1101/099143
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Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device
John R Tyson, Nigel J O'Neil, Miten Jain, Hugh E Olsen, Philip Hieter, Terrance P Snutch
bioRxiv 099143; doi: https://doi.org/10.1101/099143

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