Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case
- Published
- Accepted
- Subject Areas
- Taxonomy
- Keywords
- Vibrionaceae, Genome taxonomy, Nanopore
- Copyright
- © 2018 Tanaka et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 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.26894v1
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.
Author Comment
This is a submission to PeerJ for review.
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.