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      Whole-Genome Sequence of Francisella noatunensis subsp. orientalis Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil

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          Abstract

          This paper describes the complete genome sequence of Francisella noatunensis subsp. orientalis strain FNO01, which was isolated during the first outbreak of francisellosis in cultured Nile tilapia in Brazil. The genome is composed of a circular chromosome with 1,859,830 bp and a G+C content of ~32%.

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          CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

          Marco Galardini, Emanuele G. Biondi, Marco Bazzicalupo … (2011)
          Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping. Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes. The functionality of CONTIGuator was tested using four genomes, demonstrating its improved performances compared to currently available programs. Our approach appears efficient, with a clear visualization, allowing the user to perform comparative structural genomics analysis on draft genomes. CONTIGuator is a Python script for Linux environments and can be used on normal desktop machines and can be downloaded from http://contiguator.sourceforge.net.
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            Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity

            Settu Sridhar, Animesh Sharma, Heidi Kongshaug … (2012)
            Background Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cause mortality in aquaculture species like Atlantic cod and tilapia. We have completed the sequencing and draft assembly of the Francisella noatunensis subsp. orientalisToba04 strain isolated from farmed Tilapia. Compared to other available Francisella genomes, it is most similar to the genome of Francisella philomiragia subsp. philomiragia, a free-living bacterium not virulent to human. Results The genome is rearranged compared to the available Francisella genomes even though we found no IS-elements in the genome. Nearly 16% percent of the predicted ORFs are pseudogenes. Computational pathway analysis indicates that a number of the metabolic pathways are disrupted due to pseudogenes. Comparing the novel genome with other available Francisella genomes, we found around 2.5% of unique genes present in Francisella noatunensis subsp. orientalis Toba04 and a list of genes uniquely present in the human-pathogenic Francisella subspecies. Most of these genes might have transferred from bacterial species through horizontal gene transfer. Comparative analysis between human and fish pathogen also provide insights into genes responsible for pathogenecity. Our analysis of pseudogenes indicates that the evolution of Francisella subspecies’s pseudogenes from Tilapia is old with large number of pseudogenes having more than one inactivating mutation. Conclusions The fish pathogen has lost non-essential genes some time ago. Evolutionary analysis of the Francisella genomes, strongly suggests that human and fish pathogenic Francisella species have evolved independently from free-living metabolically competent Francisella species. These findings will contribute to understanding the evolution of Francisella species and pathogenesis.
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              Effects of temperature and salt concentration on Francisella noatunensis subsp. orientalis infections in Nile tilapia Oreochromis niloticus.

              Esteban Soto, Stephanie B Abrams, Floyd Revan (2012)
              Little is known about the environmental conditions that allow Francisella noatunensis subsp. orientalis, a worldwide emergent bacterial fish pathogen, to colonize and infect wild and cultured fish. We evaluated the effect of temperature and salinity on the infectivity of F. noatunensis subsp. orientalis in Nile tilapia Oreochromis niloticus (L). Immersion challenges of tilapia with F. noatunensis subsp. orientalis at water temperatures of 25 and 30°C in both sea and fresh water were conducted for 14 d. Morbidity and mortality were recorded daily, and at the completion of the study, a quantitative assessment of the splenic bacterial burden was performed in surviving fish. Fish maintained at 25°C developed francisellosis and had considerably higher mortality and splenic bacterial concentrations compared to control fish and fish maintained at 30°C. Moreover, increasing the water temperature from 25 to 30°C prevented the development of clinical signs and mortality in Francisella-challenged fish. In conclusion, temperature significantly influenced the development of francisellosis in tilapia, whereas salinity had no effect. Our findings may be useful in the establishment of improved prophylactic practices and in the management of outbreaks of francisellosis in the aquaculture industry.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 21 January 2016
                Publication date Collection: Jan-Feb 2016
                Volume: 4
                Issue: 1
                Electronic Location Identifier: e01603-15
                Affiliations
                [a ]AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Minas Gerais, Brazil
                [b ]Laboratory of Cellular and Molecular Genetics, Institute for Biological Science, Federal University of Minas Gerais, Minas Gerais, Brazil
                Author notes
                Address correspondence to H. C. P. Figueiredo, figueiredoh@ 123456yahoo.com .
                Article
                Publisher ID: genomeA01603-15
                DOI: 10.1128/genomeA.01603-15
                PMC ID: 4722272
                PubMed ID: 26798105
                SO-VID: 32cfc06d-08fd-446a-8327-03aa035a94b3
                Copyright © Copyright © 2016 Figueiredo et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 25 November 2015
                Date accepted : 28 November 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 5, Pages: 1, Words: 793
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date January/February 2016
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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