Rapid de novo assembly of the European eel genome from nanopore sequencing reads

Abstract

We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2 Mbp) and structural quality. This combination of affordable nanopore sequencing and light weight assembly promises to make high-quality genomic resources accessible for many non-model plants and animals.

Nanopore sequencing: Review of potential applications in functional genomics

“…In the case of plant genomes such as the fastest-growing angiosperm (greater duckweed) or tropical timber trees (teak), HMW genomic DNA extraction has been successfully performed by a CTAB method (Hoang et al, 2018;Yasodha et al, 2018), following homogenization steps to break the cell wall, where grinding with liquid nitrogen is generally used to crush the cell wall while cellular enzymes remain inactivated. For vertebrates such as clownfish or eel, suitable tissue samples such as muscles or livers are selected (Jansen et al, 2017;Tan et al, 2018). Due to the abundance of polysaccharides in plants, the CTAB method is established as the best detergent for purifying DNA from plant material (Murray & Thompson, 1980).…”

“…Likewise, in insects such as harlequin ladybird or fruit fly, a dissected tissue or a whole specimen frozen with liquid nitrogen is ground using a pestle, and HMW DNA extraction is subsequently performed with Genomic-tip 500/G kit (QIAGEN) or Blood & Cell Culture kit (QIAGEN) (Gautier et al, 2018;Miller, Staber, Zeitlinger, & Hawley, 2018). For vertebrates such as clownfish or eel, suitable tissue samples such as muscles or livers are selected (Jansen et al, 2017;Tan et al, 2018).…”

“…A successor of PBcR(Miller et al, 2008) (Koren et al, 2017) SMARTdenovo Fast and reasonably accurate OLC assembler for long reads without prior error correction step(Giordano et al, 2017) TULIP Efficient assembler for large and complex genome using seed extension(Jansen et al, 2017) Falcon Long read assembler for phased diploid genome(Chin et al, 2016) Miniasm Efficient assembler for SMRT and ONT reads without an error correction(Li, 2016) NanoSV Breakpoint junction detection of structural variant using mapping BAM file produced by LAST(Cretu Stancu et al, 2017) Sniffles Structural variation caller using automatic filtering of false events based on coverage data(Sedlazeck et al, 2018) npInv Specially designed tool for non-allelic homologous recombination (NAHR) inversions BWA-MEM Leading short read mapping tool tuned to work with ONT recently https://github.com/lh3/bwa Others NanoPipe Interactive web-based tool for fast and easy processing and analysis of the ONT data(Shabardina et al, 2019) BulkVis Visualization tool for bulk FAST5 files obtained from ONT sequencing A successor of PBcR(Miller et al, 2008) (Koren et al, 2017) SMARTdenovo Fast and reasonably accurate OLC assembler for long reads without prior error correction step(Giordano et al, 2017) TULIP Efficient assembler for large and complex genome using seed extension(Jansen et al, 2017) Falcon Long read assembler for phased diploid genome(Chin et al, 2016) Miniasm Efficient assembler for SMRT and ONT reads without an error correction(Li, 2016) NanoSV Breakpoint junction detection of structural variant using mapping BAM file produced by LAST(Cretu Stancu et al, 2017) Sniffles Structural variation caller using automatic filtering of false events based on coverage data(Sedlazeck et al, 2018) npInv Specially designed tool for non-allelic homologous recombination (NAHR) inversions BWA-MEM Leading short read mapping tool tuned to work with ONT recently https://github.com/lh3/bwa Others NanoPipe Interactive web-based tool for fast and easy processing and analysis of the ONT data(Shabardina et al, 2019) BulkVis Visualization tool for bulk FAST5 files obtained from ONT sequencing…”

Understanding and managing fish populations: keeping the toolbox fit for purpose

“…Most new technologies are currently restricted to sequencing small genomes, such as those of bacteria, but with on‐going improvements, these technologies open up the possibility of being able to sequence DNA in real‐time in the field (Hayden, ). Recently, the MinION technology has been used in hybrid assemblies with Illumina short reads (Austin et al, ) and de novo eukaryotic genomes (including fish) are in progress (Jansen et al, ).…”

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

“…Short reads then may serve for post-processing and correcting errors in a draft assembly [23]. The eel genome [9] was assembled using short reads as unique seeds that are phased and completed by Nanopore reads. While finishing this manuscript, HASLR [7] was published.…”