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      Complete Genome Sequence of an Edwardsiella piscicida-Like Species Isolated from Diseased Grouper in Israel

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          Abstract

          The Edwardsiella piscicida-like sp. is a Gram-negative facultative anaerobe that causes disease in some fish species. We report here the complete genome sequence of a virulent isolate from a diseased white grouper ( Epinephelus aeneus) raised on the Red Sea in Israel, which contains a chromosome of 3,934,167 bp and no plasmids.

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          Reducing assembly complexity of microbial genomes with single-molecule sequencing

          Background The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. Results To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Conclusions Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.
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            Edwardsiellosis in fish: a brief review.

            Edwardsiellosis is one of the most important bacterial diseases in fish. Scientific work on this disease started more than forty years ago and numerous workers around the world are continually adding to the knowledge of the disease. In spite of this, not a single article that reviews the enormous scientific data thus generated is available in the English language. This article briefly discusses some of the recent research on edwardsiellosis, describing the pathogen's interaction with the host and environment, its pathogenesis and pathology as well as diagnostic, preventive and control measures.
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              Edwardsiella piscicida sp. nov., a novel species pathogenic to fish.

              This study describes a novel species within the genus Edwardsiella based on phenotypic and genetic characterization of fish pathogenic Edwardsiella isolates previously identified as E. tarda. Phenotypic characterization, DNA-DNA hybridization and phylogenetic analysis of representative Edwardsiella isolates from fish previously identified as E. tarda were conducted and compared with E. tarda type strain (ATCC 15947(T)). Phenotypically, strains from fish grow with pin-point colonies producing slight β-haemolysis under the colony. In contrast to the E. tarda type strain, fish strains did not [corrected] degrade β-methyl-D-glucoside [corrected] (with the exception of NCIMB 2034), citric acid and L-proline. [corrected]. With the exception of strain ETK01, all fish strains were highly pathogenic to zebra fish, while ATCC 15947(T) and NCIMB 2034 were nonpathogenic. DNA-DNA hybridization (DDH) levels between representative fish isolates and the E. tarda type strain ranged from 15 to 43·6%, while NCIMB 2034 hybridised with the type strain at the level of 63·2%. DDH values between the various fish isolates ranged from 68·2 to 93·9% defining a new and separate DNA hybridization group differing from the E. tarda type strain consistent with the findings of phylogenetic analysis, in which the fish isolates comprised a separate clade. Phenotypical and genetic characterizations demonstrated that Edwardsiella isolates from fish described in this study do not belong to the species E. tarda or any of the previously established taxa within the genus Edwardsiella. The fish related strains studied here (excluding NCIMB 2034) represent, therefore, a novel species within the genus Edwardsiella for which we propose the name Edwardsiella piscicida sp. nov, with strain ET883(T) (NCIMB 14824(T) = CCUG 62929) as the type strain. The current finding will improve the diagnosis, understanding of the epidemiology and in establishment of effective control measures against this serious fish pathogen. © 2012 The Society for Applied Microbiology.
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                Author and article information

                Journal
                Genome Announc
                Genome Announc
                ga
                ga
                GA
                Genome Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2169-8287
                23 July 2015
                Jul-Aug 2015
                : 3
                : 4
                : e00829-15
                Affiliations
                [a ]College of Veterinary Medicine, Mississippi State University, Mississippi, USA
                [b ]USDA-ARS Warmwater Aquaculture Center, Stoneville, Mississippi, USA
                [c ]Israel Oceanographic and Limnological Research, National Center for Mariculture, Eilat, Israel
                [d ]School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
                Author notes
                Address correspondence to Matt J. Griffin, matt.griffin@ 123456msstate.edu .
                Article
                genomeA00829-15
                10.1128/genomeA.00829-15
                4513164
                26205870
                8869f8e8-591c-4e81-b0aa-4f5b573275f7
                Copyright © 2015 Reichley et al.

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

                History
                : 17 June 2015
                : 22 June 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 20, Pages: 2, Words: 1580
                Categories
                Prokaryotes
                Custom metadata
                July/August 2015
                free

                Genetics
                Genetics

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