Complete Genome Assembly and Comparative Genomic of Yeast Strains using the MinION device

Recently, Oxford Nanopore Technologies Ltd commercialized the MinION device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments. The Oxford Nanopore technology is truly disruptive and can sequence small genomes in a manner of seconds. It has the potential to revolutionize genomic applications due to its portability, low-cost and ease of use, compared to existing long reads sequencing technologies. Today, the MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as Saccharomyces cerevisiae (yeast) genome. Combined with existing assembler algorithms, it allows to generate near complete genome assemblies and to perform comparative genomic analyses, including the analyses of repetitive regions. Here, we resequenced the S288C yeast strain to evaluate the performance of nanopore-only assemblers, and then de novo sequence and assemble 21 strains of S. cerevisiae using the MinION platform. The contiguity of our assemblies is fourteen times higher than illumina-only assemblies and we obtained one or two contigs for 65% of the chromosomes. We accurately detected large structural variations across the 22 strains. Moreover, due to the high contiguity and completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect tandemly duplicated gene families that are generally missed in illumina-only assemblies.