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      Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Diseased Ayu (Plecoglossus altivelis altivelis) Caught at Three Sites in the Kagami River in Kochi, Japan

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          Abstract

          Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae. Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

          ABSTRACT

          Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae. Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

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          DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

          Yasuhiro Tanizawa, Takatomo Fujisawa, Yasukazu Nakamura (2017)
          Abstract Summary We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future. Availability and implementation The software is implemented in Python 3 and runs in both Python 2.7 and 3.4—on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/. Contact yn@nig.ac.jp Supplementary information Supplementary data are available at Bioinformatics online.
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            Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan

            Erina Fujiwara-Nagata, Céline Chantry-Darmon, Jean-François Bernardet … (2013)
            The bacterium Flavobacterium psychrophilum is a serious problem for salmonid farming worldwide. This study investigates by multilocus sequence typing (MLST) the population structure of this pathogen in Japan where it is also a major concern for ayu, a popular game fish related to salmoniforms. A total of 34 isolates collected across the country and 80 isolates sampled in a single model river by electrofishing were genotyped. The data accounting for 15 fish species allowed identifying 35 distinct sequence types (ST) in Japan. These ST are distinct from those reported elsewhere, except for some ST found in rainbow trout and coho salmon, two fish that have been the subject of intensive international trade. The pattern of polymorphism is, however, strikingly similar across geographical scales (model river, Japan, world) in terms of the fraction of molecular variance linked to the fish host (~50%) and of pairwise nucleotide diversity between ST (~5 Kbp-1). These observations go against the hypothesis of a recent introduction of F. psychrophilum in Japan. Two findings were made that are important for disease control: 1) at least two independent F. psychrophilum lineages infect ayu and 2) co-infections of the same individual fish by different strains occur.
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              Outbreaks of Coldwater Disease in Wild Ayu and Pale Chub.

              Yoshisuke Iida, Akio Mizokami (1996)
              Article 0 comments Cited 12 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                David A. Baltrus: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic): 22 August 2019
                Publication date Collection: August 2019
                Volume: 8
                Issue: 34
                Electronic Location Identifier: e00773-19
                Affiliations
                [a ]Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi, Japan
                [b ]Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
                [c ]School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
                [d ]Laboratory of Fish Disease, Aquaculture Course, Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
                University of Arizona
                Author notes
                Address correspondence to Masayuki Imajoh, m-imajoh@ 123456kochi-u.ac.jp .

                Citation Yamashita H, Wada T, Kato Y, Ikeda T, Imajoh M. 2019. Draft genome sequences of three Flavobacterium psychrophilum strains isolated from diseased ayu ( Plecoglossus altivelis altivelis) caught at three sites in the Kagami River in Kochi, Japan. Microbiol Resour Announc 8:e00773-19. https://doi.org/10.1128/MRA.00773-19.

                Article
                Publisher ID: MRA00773-19
                DOI: 10.1128/MRA.00773-19
                PMC ID: 6706692
                PubMed ID: 31439700
                SO-VID: 9465bf25-7323-4af0-b385-aa2eb0f97625
                Copyright © Copyright © 2019 Yamashita et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 1 July 2019
                Date accepted : 29 July 2019
                Page count
                Figures: 0, Tables: 1, Equations: 0, References: 5, Pages: 3, Words: 1126
                Funding
                Funded by: the Kochi University Research Project;
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date August 2019

                Data availability:

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