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      Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1 T)

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          Abstract

          Parvibaculum lavamentivorans DS-1 T is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1 T is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

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          Most cited references44

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          Gene Ontology: tool for the unification of biology

          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.

            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.

              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
                Stand Genomic Sci
                Stand Genomic Sci
                SIGS
                Standards in Genomic Sciences
                Michigan State University
                1944-3277
                22 December 2011
                31 December 2011
                : 5
                : 3
                : 298-310
                Affiliations
                [1 ]Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany
                [2 ]DOE Joint Genome Institute, Walnut Creek, California, USA
                [3 ]Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
                [4 ]Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
                [5 ]Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
                Author notes
                Article
                sigs.2215005
                10.4056/sigs.2215005
                3368416
                22675581
                57683c8b-27a0-48a2-893c-4d5ea17b497f
                Copyright @ 2011

                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 work is properly cited.

                History
                Funding
                Funded by: Deutsche Forschungsgemeinschaft
                Award ID: DFG grant SCHL 1936/1-1
                Funded by: Office of Science of the U.S. Department of Ener
                Award ID: DE-AC02-05CH11231
                Award ID: W-7405-Eng-48
                Award ID: DE-AC03-76SF00098
                Award ID: . W-7405-ENG-36
                Categories
                Short Genome Reports

                Genetics
                aerobic,rhodobiaceae,parvibaculum lavamentivorans ds-1,gram-negative,surfactant biodegradation

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