Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case
A peer-reviewed article of this Preprint also exists.
Author and article information
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 genomesequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minim al laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae, compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species; Vibrio aphrogenes,V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Overall genome relatedness indices (OGRI) based on Nanopore-only assembly were compared with that of Illumina and hybrid assemblies. Our dataset showed that indels in Nanopore-only assemblies does not influence the species discrimination of these five Vibrio species, suggesting the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI.
Cite this as
2018. Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case. PeerJ Preprints 6:e26894v1 https://doi.org/10.7287/peerj.preprints.26894v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a submission to PeerJ for review.
Sections
Supplemental Information
Heatmap representation of in silico DDH values using different assemblies
in silico DDH (DNA-DNA hybridization) values were estimated using Genome-to-Genome Distance Calculator (GGDC) 2.1 (Nelder & Wedderburn, 1972; Meier-Kolthoff et al., 2013) and the values represented here are calculated according to formula 2 (recommended).
Phylogenetic reconstruction using eight protein-coding gene nucleotide sequences from hybridand Nanopore-only assemblies
Trees were reconstructed using RAxML 8.2.11 (Stamatakis, 2014) with the GTRGAMMA model and 500 bootstrap replications. The final trees were prepared using FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/).
Data statistics for the reads used in Vibrio aphrogenes assemblies
Basic information of the data used to assemble V. aphrogenes genome. The genome was sequenced in four different methods; SMRT system from Pacific Biosciences (PacBio), MinION from Oxford Nanopore Technologies (MinION), mate-pair (MiSeq-MP) and paired-end (MiSeq-PE) reads from Illumina MiSeq. For MinION, the data shown here is after debarcoding with Porechop 0.2.2 (https://github.com/rrwick/Porechop) with --untrimmed option.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Mami Tanaka conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Sayaka Mino performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Yoshitoshi Ogura performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Tetsuya Hayashi contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Tomoo Sawabe conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Raw data and assembled genomes are deposited in DDBJ/EMBL/GenBank under BioProject PRJDB5783 involving BioSamples SAMD00080445, SAMD00057777, SAMD00080446, SAMD00116203, and SAMD00080447, for V. algivorus, V. aphrogenes, V. casei, V. litoralis, and V. rumoiensis, respectively.
Data Deposition
The following information was supplied regarding data availability:
Raw data and assembled genomes are deposited in DDBJ/EMBL/GenBank under BioProject PRJDB5783 involving BioSamples SAMD00080445, SAMD00057777, SAMD00080446, SAMD00116203, and SAMD00080447, for V. algivorus, V. aphrogenes, V. casei, V. litoralis, and V. rumoiensis, respectively.
Funding
This work was partly supported by Kaken (16H04976). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
