Joseph Schacherer│Yeast genome assembly and structural variant mapping using Nanopore sequencing скачать в хорошем качестве

Joseph Schacherer│Yeast genome assembly and structural variant mapping using Nanopore sequencing

Comprehensive genomic variant maps are essential to explore genome evolution as well as its phenotypic consequences in natural populations. To date, short-read sequencing allowed to have genome- and species-wide views of mainly single nucleotide and copy number variants as we recently obtained in the Saccharomyces cerevisiae species by whole genome sequencing of 1,011 natural (1002genomes.u-strasbg.fr/) isolates using an Illumina technology. However, the detection of structural variants (e.g. long indels, inversions, translocations) (SVs) still poses challenges, more precisely when variants are in high complexity regions while they correspond to genetic variants underlying phenotypic variation. Emerging long-read sequencing technologies, such as Oxford Nanopore MinION sequencing, provide an unprecedented opportunity to efficiently detect these structural variants. To evaluate the performance of this technology for whole-genome assembly and SVs detection, we resequenced various genomes of natural isolates of two distinct yeast species, namely Saccharomyces cerevisiae and Dekkera bruxellensis, showing different degree of genomic complexities. Using the ONT MinION at 20x mean coverage, highly complete and contiguous assemblies have been obtained. Data generated allowed hence to accurately detect SVs, such as translocations and large inversions throughout the genomes. Among the long inserted and deleted regions, we identified those related to transposable elements and could provide a complete cartography of these elements among the sequenced isolates. Our preliminary results clearly show the value of the MinION system for screening whole genomes for complex SVs and deeply characterizing genome architecture in yeast natural populations. Flongle, GridION, MinION, MinIT, PromethION, and VolTRAX are currently for research use only.