Hokkaido University Collection of Scholarly and Academic Papers >
Graduate School of Fisheries Sciences / Faculty of Fisheries Sciences >
Peer-reviewed Journal Articles, etc >
Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis Glade species as a test case
This item is licensed under:Creative Commons Attribution 4.0 International
Title: | Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis Glade species as a test case |
Authors: | Tanaka, Mami Browse this author | Mino, Sayaka Browse this author | Ogura, Yoshitoshi Browse this author | Hayashi, Tetsuya Browse this author | Sawabe, Tomoo Browse this author →KAKEN DB |
Keywords: | Vibrionaceae | Genome taxonomy | Nanopore |
Issue Date: | 18-Jun-2018 |
Publisher: | PeerJ |
Journal Title: | Peerj |
Volume: | 6 |
Start Page: | e5018 |
Publisher DOI: | 10.7717/peerj.5018 |
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 gnome 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 gnomes of fiw Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall gnome 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 frorn Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA. |
Rights: | https://creativecommons.org/licenses/by/4.0/ |
Type: | article |
URI: | http://hdl.handle.net/2115/71059 |
Appears in Collections: | 水産科学院・水産科学研究院 (Graduate School of Fisheries Sciences / Faculty of Fisheries Sciences) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
|
Submitter: 澤辺 智雄
|