Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics

Rumoiensis clade species as a test case

Mami Tanaka, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Tomoo Sawabe

Research output: Contribution to journalArticle

Abstract

Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

Original languageEnglish
Article numbere5018
JournalPeerJ
Volume2018
Issue number6
DOIs
Publication statusPublished - Jan 1 2018

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Vibrionaceae
Nanopores
Taxonomies
Genes
Availability
Genome
taxonomy
genome
Multilocus Sequence Typing
testing
Vibrio rumoiensis
Bacterial Genomes
Vibrio
nanopores
DNA
Base Composition
Computer Simulation
nucleic acid hybridization
topology
Nucleotides

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics : Rumoiensis clade species as a test case. / Tanaka, Mami; Mino, Sayaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Sawabe, Tomoo.

In: PeerJ, Vol. 2018, No. 6, e5018, 01.01.2018.

Research output: Contribution to journalArticle

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