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      New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing

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          ABSTRACT

          The acquisition of Photorhabdus insect-related (Pir) toxin-like genes in Vibrio parahaemolyticus has been linked to hepatopancreatic necrosis disease in shrimp. We report the whole-genome sequences of genetically virulent and avirulent V. parahaemolyticus isolated from a Malaysian aquaculture pond and show that they represent previously unreported sequence types of V. parahaemolyticus.

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          Toward almost closed genomes with GapFiller

          Marten Boetzer, Walter Pirovano (2012)
          De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
          Article 0 comments Cited 653 times – based on 0 reviews     Review now
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            SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

            Marten Boetzer, Walter Pirovano (2014)
            Background The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data. Results Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes. Conclusions The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner.
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              Photorhabdus insect-related (Pir) toxin-like genes in a plasmid of Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (AHPND) of shrimp.

              Jee Han, Kathy Tang, Loc H Tran … (2015)
              The 69 kb plasmid pVPA3-1 was identified in Vibrio parahaemolyticus strain 13‑028/A3 that can cause acute hepatopancreatic necrosis disease (AHPND). This disease is responsible for mass mortalities in farmed penaeid shrimp and is referred to as early mortality syndrome (EMS). The plasmid has a GC content of 45.9% with a copy number of 37 per bacterial cell as determined by comparative quantitative PCR analyses. It consists of 92 open reading frames that encode mobilization proteins, replication enzymes, transposases, virulence-associated proteins, and proteins similar to Photorhabdus insect-related (Pir) toxins. In V. parahaemolyticus, these Pir toxin-like proteins are encoded by 2 genes (pirA- and pirB-like) located within a 3.5 kb fragment flanked with inverted repeats of a transposase-coding sequence (1 kb). The GC content of these 2 genes is only 38.2%, substantially lower than that of the rest of the plasmid, which suggests that these genes were recently acquired. Based on a proteomic analysis, the pirA-like (336 bp) and pirB-like (1317 bp) genes encode for 13 and 50 kDa proteins, respectively. In laboratory cultures of V. parahaemolyticus 13-028/A3, both proteins were secreted into the culture medium. We developed a duplex PCR diagnostic method, with a detection limit of 10(5) CFU ml(-1) and targeting pirA- and pirB-like genes in this strain of V. parahaemolyticus. This PCR protocol can reliably detect AHPND-causing strains of V. parahaemolyticus and does not cross react with non-pathogenic strains or with other species of Vibrio isolated from shrimp ponds.
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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): 11 May 2017
                Publication date Collection: May 2017
                Volume: 5
                Issue: 19
                Electronic Location Identifier: e00302-17
                Affiliations
                [a ]School of Science, Monash University Malaysia, Petaling Jaya, Malaysia
                [b ]Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Malaysia
                Author notes
                Address correspondence to Han Ming Gan, gan.han.ming@ 123456monash.edu .
                Article
                Publisher ID: genomeA00302-17
                DOI: 10.1128/genomeA.00302-17
                PMC ID: 5427208
                PubMed ID: 28495773
                SO-VID: 18734b4c-8783-4e0c-9574-72f711b10c34
                Copyright © Copyright © 2017 Foo 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 : 14 March 2017
                Date accepted : 16 March 2017
                Page count
                Figures: 0, Tables: 1, Equations: 0, References: 10, Pages: 3, Words: 1276
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date May 2017

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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