Supporting data for "de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer"
Dataset type: Genomic
Data released on December 23, 2016
Istace B; Friedrich A; d’Agata L; Faye S; Payen E; Beluche O; Caradec C; Davidas S; Cruaud C; Liti G; Lemainque A; Engelen S; Wincker P; Schacherer J; Aury JM (2016): Supporting data for "de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer" GigaScience Database. http://dx.doi.org/10.5524/100263
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.
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Additional details
Read the peer-reviewed publication(s):
(PubMed: 28369459)
Accessions (data generated as part of this study):
BioProject:
PRJEB14774
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
ABH | 1337530 | Saccharomyces cerevisiae | Description:YJM454_1b, Saccharomyces cerevisiae, i... Alternative accession-BioSample:SAMEA3894921 Source material identifiers:not applicable ... + | ||
ADM | 929629 | Saccharomyces cerevisiae CLIB324 | Saccharomyces cerevisiae CLIB324 | Description:CLIB324_2, Saccharomyces cerevisiae, i... Alternative accession-BioSample:SAMEA3894961 Source material identifiers:not applicable ... + | |
ADQ | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:K12_2, Saccharomyces cerevisiae, isola... Alternative accession-BioSample:SAMEA3894964 Source material identifiers:not applicable ... + |
ADS | 471859 | Saccharomyces cerevisiae | Description:T73_1b, Saccharomyces cerevisiae, isol... Alternative accession-BioSample:SAMEA3894966 Source material identifiers:not applicable ... + | ||
AEG | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:CBS7962, Saccharomyces cerevisiae, iso... Alternative accession-BioSample:SAMEA3894974 Source material identifiers:not applicable ... + |
AKR | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:CLQCA_05-006, Saccharomyces cerevisiae... Alternative accession-BioSample:SAMEA3895070 Source material identifiers:not applicable ... + |
ANE | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:YPS134, Saccharomyces cerevisiae, isol... Alternative accession-BioSample:SAMEA3895112 Source material identifiers:not applicable ... + |
ASN | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:CLIB630, Saccharomyces cerevisiae, iso... Alternative accession-BioSample:SAMEA3895186 Source material identifiers:not applicable ... + |
AVB | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:CECT10266, Saccharomyces cerevisiae, i... Alternative accession-BioSample:SAMEA3895205 Source material identifiers:not applicable ... + |
BAH | 4932 | brewer's yeast | baker's yeast | Saccharomyces cerevisiae | Description:SX3, Saccharomyces cerevisiae, isolate... Alternative accession-BioSample:SAMEA3895227 Source material identifiers:not applicable ... + |