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      An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

      research-article
      Author(s): 1 , 1 , 1 ,
      Publication date (Electronic):
      Journal: Standards in Genomic Sciences
      Publisher: BioMed Central
      Keywords: Roseobacter, DMSP

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          Abstract

          When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome.

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          Most cited references33

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          Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

          C Woese, O Kandler, M L Wheelis (1990)
          Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
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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.
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              Overview of the marine roseobacter lineage.

              Alison Buchan, José González, Mary Ann Moran (2005)
              Article 0 comments Cited 254 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Adam R Rivers
                Christa B Smith
                Mary Ann Moran
                Journal
                Journal ID (nlm-ta): Stand Genomic Sci
                Journal ID (iso-abbrev): Stand Genomic Sci
                Title: Standards in Genomic Sciences
                Publisher: BioMed Central
                ISSN (Electronic): 1944-3277
                Publication date Collection: 2014
                Publication date (Electronic): 8 December 2014
                Volume: 9
                Page: 11
                Affiliations
                [1 ]Department of Marine Sciences, University of Georgia, Athens, GA, USA
                Article
                Publisher ID: 1944-3277-9-11
                DOI: 10.1186/1944-3277-9-11
                PMC ID: 4334477
                PubMed ID: 25780504
                SO-VID: 2cf16f55-b45d-426e-867e-da220e8015ed
                Copyright © Copyright © 2014 Rivers et al.; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 12 June 2014
                Date accepted : 16 June 2014
                Categories
                Subject: Short Genome Report

                ScienceOpen disciplines: Genetics
                Keywords: roseobacter,dmsp
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: roseobacter, dmsp

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