De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.

Benjamin Istace,Patrick Wincker,Stefan Engelen,Sabrina Davidas,Claudia Caradec,Odette Beluche,Léo D'Agata,Anne Friedrich,Sébastien Faye,Jean-Marc Aury,Arnaud Lemainque,Joseph Schacherer,Corinne Cruaud,Emilie Payen,Gianni Liti

doi:10.1093/gigascience/giw018

Abstract

Background: 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. Results: 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. Conclusion: 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.

Highlights

Today, long-read sequencing technology offers interesting alternatives to solve genome assembly difficulties and improve the completeness of genome assemblies, mostly in repetitive regions (Jain et al 2015) where short-read sequencing has failed
2.3 Gb and 63% of the nucleotides were in 2D reads, which represented a 187x and 118x genome coverage for 1D and 2D reads, respectively
The results of this analysis indicate that the error rate of the Oxford Nanopore Technology (ONT) R7.3 reads was in the range that is obtained using existing long-read technologies

Summary

Introduction

Long-read sequencing technology offers interesting alternatives to solve genome assembly difficulties and improve the completeness of genome assemblies, mostly in repetitive regions (Jain et al 2015) where short-read sequencing has failed. The cost of the commercially available Pacific Biosystems RS II instrument is high and the infrastructure and implementation needs make it inaccessible to large sections of the research community This year Oxford Nanopore Technologies Ltd (ONT, Oxford, UK) commercialized MinION, a single-molecule nanopore sequencer that can be connected to a laptop through a USB interface (Loman and Watson 2015; Deamer et al 2016). This system is portative (close to the size of a harmonica) and low-cost (currently USD 1,000 for the instrument). The MinION technology is based on an array of nanopores embedded on a chip that detects consecutive 6-

Methods

Results

Conclusion