Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case
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 Technologie...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2018-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/5018.pdf |
| _version_ | 1797419846143574016 |
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| author | Mami Tanaka Sayaka Mino Yoshitoshi Ogura Tetsuya Hayashi Tomoo Sawabe |
| author_facet | Mami Tanaka Sayaka Mino Yoshitoshi Ogura Tetsuya Hayashi Tomoo Sawabe |
| author_sort | Mami Tanaka |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:54:08Z |
| format | Article |
| id | doaj.art-62fcfe200c3e4b919c520bab768a230d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:54:08Z |
| publishDate | 2018-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-62fcfe200c3e4b919c520bab768a230d2023-12-03T10:14:04ZengPeerJ Inc.PeerJ2167-83592018-06-016e501810.7717/peerj.5018Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test caseMami Tanaka0Sayaka Mino1Yoshitoshi Ogura2Tetsuya Hayashi3Tomoo Sawabe4Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, JapanLaboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, JapanDepartment of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, JapanLaboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, JapanWhole 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.https://peerj.com/articles/5018.pdfVibrionaceaeGenome taxonomyNanopore |
| spellingShingle | Mami Tanaka Sayaka Mino Yoshitoshi Ogura Tetsuya Hayashi Tomoo Sawabe Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case PeerJ Vibrionaceae Genome taxonomy Nanopore |
| title | Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case |
| title_full | Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case |
| title_fullStr | Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case |
| title_full_unstemmed | Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case |
| title_short | Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case |
| title_sort | availability of nanopore sequences in the genome taxonomy for vibrionaceae systematics rumoiensis clade species as a test case |
| topic | Vibrionaceae Genome taxonomy Nanopore |
| url | https://peerj.com/articles/5018.pdf |
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