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Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case

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203 days ago
Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case https://t.co/ATbEVcKTy8
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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).

DOI: 10.7287/peerj.preprints.26894v1/supp-1

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/).

DOI: 10.7287/peerj.preprints.26894v1/supp-2

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.

DOI: 10.7287/peerj.preprints.26894v1/supp-3

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.


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