title: de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.
abstract: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; 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 contiguity allowed us to accurately detect large structural variations across the 21 studied genomes.
  
  
  
  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. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology.
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Istace
authors.affiliation: Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Friedrich
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Léo
authors.initials: L
authors.lastname: d'Agata
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Faye
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Payen
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Odette
authors.initials: O
authors.lastname: Beluche
authors.affiliation: Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
authors.forename: Claudia
authors.initials: C
authors.lastname: Caradec
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Davidas
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Cruaud
authors.affiliation: Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France.
authors.forename: Gianni
authors.initials: G
authors.lastname: Liti
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Lemainque
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Engelen
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.|Université d'Evry Val d'Essonne, UMR 8030, CP5706, 91057 Evry, France.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, 91057 Evry, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
authors.forename: Joseph
authors.initials: J
authors.lastname: Schacherer
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
mesh_terms: D015825:Chromosomes, Fungal; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements; D004271:DNA, Fungal; D018628:Gene Dosage; D016681:Genome, Fungal; D054629:Genome, Mitochondrial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D015003:Yeasts / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D004271:DNA, Fungal
keywords: Genome finishing; MinION device; Nanopore sequencing; Oxford Nanopore; Structural variations; Transposable elements; de novo assembly