Dataset Information

Complete Genome Sequence of a Streptococcus pyogenes Serotype M12 Scarlet Fever Outbreak Isolate from China, Compiled Using Oxford Nanopore and Illumina Sequencing.

ABSTRACT: The incidence of scarlet fever cases remains high in China. Here, we report the complete genome sequence of a Streptococcus pyogenes isolate of serotype M12, which has been confirmed as the predominant serotype in recent outbreaks. Genome sequencing was achieved by a combination of Oxford Nanopore MinION and Illumina methodologies.

SUBMITTER: You Y

PROVIDER: S-EPMC5940962 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Complete Genome Sequence of a Streptococcus pyogenes Serotype M12 Scarlet Fever Outbreak Isolate from China, Compiled Using Oxford Nanopore and Illumina Sequencing.

You Yuanhai Y Kou Yongjun Y Niu Longfei L Jia Qiong Q Liu Yahui Y Davies Mark R MR Walker Mark J MJ Zhu Jiaqiang J Zhang Jianzhong J

Genome announcements 20180503 18

The incidence of scarlet fever cases remains high in China. Here, we report the complete genome sequence of a <i>Streptococcus pyogenes</i> isolate of serotype M12, which has been confirmed as the predominant serotype in recent outbreaks. Genome sequencing was achieved by a combination of Oxford Nanopore MinION and Illumina methodologies. ...[more]

PMID: 29724853

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Project description:BackgroundStructural variants (SVs), including deletions, insertions, duplications, and inversions, are relatively long genomic variations implicated in a diverse range of processes from human disease to ecology and evolution. Given their complex signatures, tendency to occur in repeated regions, and large size, discovering SVs based on short reads is challenging compared to single-nucleotide variants. The increasing availability of long-read technologies has greatly facilitated SV discovery; however, these technologies remain too costly to apply routinely to population-level studies. Here, we combined short-read and long-read sequencing technologies to provide a comprehensive population-scale assessment of structural variation in a panel of Canadian soybean cultivars.ResultsWe used Oxford Nanopore long-read sequencing data (~12× mean coverage) for 17 samples to both benchmark SV calls made from Illumina short-read data and predict SVs that were subsequently genotyped in a population of 102 samples using Illumina data. Benchmarking results show that variants discovered using Oxford Nanopore can be accurately genotyped from the Illumina data. We first use the genotyped deletions and insertions for population genetics analyses and show that results are comparable to those based on single-nucleotide variants. We observe that the population frequency and distribution within the genome of deletions and insertions are constrained by the location of genes. Gene Ontology and PFAM domain enrichment analyses also confirm previous reports that genes harboring high-frequency deletions and insertions are enriched for functions in defense response. Finally, we discover polymorphic transposable elements from the deletions and insertions and report evidence of the recent activity of a Stowaway MITE.ConclusionsWe show that structural variants discovered using Oxford Nanopore data can be genotyped with high accuracy from Illumina data. Our results demonstrate that long-read and short-read sequencing technologies can be efficiently combined to enhance SV analysis in large populations, providing a reusable framework for their study in a wider range of samples and non-model species.

Project description:BACKGROUND:We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing by determining genome completeness and accuracy, antimicrobial resistance (AMR), virulence potential, multilocus sequence typing (MLST), phylogeny, and pan genome. Ten bacterial species (10 strains) were tested for simulated reads of both mediocre- and low-quality, whereas 11 bacterial species (12 strains) were tested for real reads. RESULTS:Unicycler performed the best for achieving contiguous genomes, closely followed by MaSuRCA, while all SPAdes assemblies were incomplete. MaSuRCA was less tolerant of low-quality long reads than SPAdes and Unicycler. The hybrid assemblies of five antimicrobial-resistant strains with simulated reads provided consistent AMR genotypes with the reference genomes. The MaSuRCA assembly of Staphylococcus aureus with real reads contained msr(A) and tet(K), while the reference genome and SPAdes and Unicycler assemblies harbored blaZ. The AMR genotypes of the reference genomes and hybrid assemblies were consistent for the other five antimicrobial-resistant strains with real reads. The numbers of virulence genes in all hybrid assemblies were similar to those of the reference genomes, irrespective of simulated or real reads. Only one exception existed that the reference genome and hybrid assemblies of Pseudomonas aeruginosa with mediocre-quality long reads carried 241 virulence genes, whereas 184 virulence genes were identified in the hybrid assemblies of low-quality long reads. The MaSuRCA assemblies of Escherichia coli O157:H7 and Salmonella Typhimurium with mediocre-quality long reads contained 126 and 118 virulence genes, respectively, while 110 and 107 virulence genes were detected in their MaSuRCA assemblies of low-quality long reads, respectively. All approaches performed well in our MLST and phylogenetic analyses. The pan genomes of the hybrid assemblies of S. Typhimurium with mediocre-quality long reads were similar to that of the reference genome, while SPAdes and Unicycler were more tolerant of low-quality long reads than MaSuRCA for the pan-genome analysis. All approaches functioned well in the pan-genome analysis of Campylobacter jejuni with real reads. CONCLUSIONS:Our research demonstrates the hybrid assembly pipeline of Unicycler as a superior approach for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.

Dataset Information

Complete Genome Sequence of a Streptococcus pyogenes Serotype M12 Scarlet Fever Outbreak Isolate from China, Compiled Using Oxford Nanopore and Illumina Sequencing.

Publications

Complete Genome Sequence of a Streptococcus pyogenes Serotype M12 Scarlet Fever Outbreak Isolate from China, Compiled Using Oxford Nanopore and Illumina Sequencing.

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