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      Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9 T) and comparison to “ Dehalococcoides” strains

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          Abstract

          Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming, Gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) a phylogenetic position that is distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9 T contains 1,720 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small subunit rRNA (16S) locus.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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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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                Author and article information

                Journal
                Journal ID (nlm-ta): Stand Genomic Sci
                Journal ID (iso-abbrev): Stand Genomic Sci
                Journal ID (publisher-id): SIGS
                Title: Standards in Genomic Sciences
                Publisher: Michigan State University
                ISSN (Electronic): 1944-3277
                Publication date (Electronic): 15 May 2012
                Publication date Collection: 25 May 2012
                Volume: 6
                Issue: 2
                Pages: 251-264
                Affiliations
                [1 ]Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
                [2 ]DOE Joint Genome Institute, Walnut Creek, California, USA
                [3 ]Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
                [4 ]Lawrence Berkeley National Laboratory, Berkeley, California, USA
                [5 ]Louisiana State University, Baton Rouge, Louisiana, USA
                [6 ]Department of Life Sciences, University of Coimbra, Coimbra, Portugal
                [7 ]University of Alaska Anchorage, Anchorage, Alaska, USA
                Author notes
                [* ]Corresponding author: William M. Moe
                Article
                Publisher ID: sigs.2806097
                DOI: 10.4056/sigs.2806097
                PMC ID: 3387798
                PubMed ID: 22768368
                SO-VID: f305a68f-dbb8-41c6-b3ab-a4478957af96
                Copyright statement: Copyright @ 2012
                History
                Funding
                Funded by: Office of Science of the U.S. Department of Energy
                Funded by: DE-AC02-05CH11231
                Categories
                Subject: Short Genome Reports

                ScienceOpen disciplines: Genetics
                Keywords: contamination,hydrogen utilization,reductive dechlorination,chloroflexi,groundwater,strictly anaerobic
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: contamination, hydrogen utilization, reductive dechlorination, chloroflexi, groundwater, strictly anaerobic

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