RT Journal Article SR Electronic T1 de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer JF bioRxiv FD Cold Spring Harbor Laboratory SP 066613 DO 10.1101/066613 A1 Benjamin Istace A1 Anne Friedrich A1 Léo d’Agata A1 Sébastien Faye A1 Emilie Payen A1 Odette Beluche A1 Claudia Caradec A1 Sabrina Davidas A1 Corinne Cruaud A1 Gianni Liti A1 Arnaud Lemainque A1 Stefan Engelen A1 Stefan Engelen A1 Patrick Wincker A1 Joseph Schacherer A1 Jean-Marc Aury YR 2016 UL http://biorxiv.org/content/early/2016/07/28/066613.abstract AB Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small and low-cost single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments. The Oxford Nanopore technology is truly disruptive and can sequence small genomes in a matter of seconds. It has the potential to revolutionize genomic applications due to its portability, low-cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65% of the chromosomes. This high continuity allowed us to accurately detect large structural variations across the 21 studied genomes. Moreover, because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy.ONTOxford Nanopore TechnologySMRTSingle-Molecule Real-Time SequencingUSBUniversal Serial BusMtMitochondrialLTRLong Terminal RepeatSNPSingle Nucleotide PolymorphismORFOpen Reading FrameMAPMinION Access Programme