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      • Record: found
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      Is Open Access

      The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

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          Abstract

          Background

          Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general.

          Methodology/Principal Findings

          We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb).

          Conclusions/Significance

          The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.

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          Most cited references140

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          Cluster analysis and display of genome-wide expression patterns.

          P. T. Spellman, P. O. Brown, D Botstein … (1998)
          A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be interpreted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly characterized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently.
          Article 0 comments Cited 1865 times – based on 0 reviews     Review now
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            The Pfam protein families database.

            A. Bateman, Lachlan Coin (2004)
            Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).
            Article 0 comments Cited 1104 times – based on 0 reviews     Review now
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              The minimum information about a genome sequence (MIGS) specification.

              Dawn Field, George Garrity, Tanya Gray … (2008)
              With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
              Article 0 comments Cited 822 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                : Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2010
                Publication date (Electronic): 19 March 2010
                Volume: 5
                Issue: 3
                Electronic Location Identifier: e9605
                Affiliations
                [1 ]Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
                [2 ]The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
                [3 ]Institut de Génétique et Microbiologie, Université Paris-Sud, Paris, France
                [4 ]Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
                [5 ]Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
                [6 ]Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
                [7 ]Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
                [8 ]Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
                [9 ]UC Davis Genome Center, University of California Davis, Davis, California, United States of America
                [10 ]Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
                [11 ]Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
                [12 ]Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
                [13 ]Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
                Miami University, United States of America
                Author notes

                Conceived and designed the experiments: ALH CN HMK FP JAE. Performed the experiments: ALH CN RM JRR HMK FP JAE. Analyzed the data: ALH CN JHB SD SH RM QR TL JMF MP CD FP TA JAE. Contributed reagents/materials/analysis tools: ALH JHB RM JAE. Wrote the paper: ALH CN JMF MP FP TA JAE. Designed and ran the APIS software: JHB. Coordinated initial annotation of the genome: RM. Performed genome finishing: JRR. Coordinated genome finishing: HMK. Analyzed transporter related functions: QR. Analyzed non coding RNAs: TL. Coordinated reannotation of the genome: FP.

                [¤]

                Current address: J. Craig Venter Institute, Rockville, Maryland, United States of America

                Article
                Publisher ID: 09-PONE-RA-12854R1
                DOI: 10.1371/journal.pone.0009605
                PMC ID: 2841640
                PubMed ID: 20333302
                SO-VID: 27bf7773-6175-4020-a678-5b33648ceac8
                Copyright © Hartman et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                Date received : 24 July 2009
                Date accepted : 11 February 2010
                Page count
                Pages: 20
                Categories
                Subject: Research Article
                Subject: Biotechnology/Applied Microbiology
                Subject: Computational Biology/Comparative Sequence Analysis
                Subject: Computational Biology/Genomics
                Subject: Genetics and Genomics/Genome Projects
                Subject: Genetics and Genomics/Microbial Evolution and Genomics
                Subject: Microbiology/Environmental Microbiology
                Subject: Microbiology/Microbial Evolution and Genomics
                Subject: Microbiology/Microbial Physiology and Metabolism
                Subject: Molecular Biology/Bioinformatics
                Subject: Molecular Biology/Chromosome Structure
                Subject: Molecular Biology/DNA Repair
                Subject: Molecular Biology/Molecular Evolution

                ScienceOpen disciplines: Uncategorized
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                ScienceOpen disciplines: Uncategorized

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