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      Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1

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          Abstract

          Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation. The genome consists of a 5,547,747 bp chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and 23,681 bp, respectively. In total, 5,588 genes were predicted and annotated.

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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 (publisher-id): SIGS
                Title: Standards in Genomic Sciences
                Publisher: Michigan State University
                ISSN (Electronic): 1944-3277
                Publication date (Electronic): 01 October 2011
                Publication date Collection: 15 October 2011
                Volume: 5
                Issue: 1
                Pages: 144-153
                Affiliations
                [1 ]Sector of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
                [2 ]DOE Joint Genome Institute, Walnut Creek, California, USA
                [3 ]Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
                [4 ]Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, 15701, Athens, Greece
                [5 ]Centre for Bioinformatics, Department of Informatics, School of Natural & Mathematical Sciences, King's College London (KCL), London WC2R 2LS, UK
                [§ ]Present address: Computational Genomics Unit, Institute of Agrobiotechnology, Center for Research & Technology Hellas (CERTH), GR-57001 Thessaloniki, Greece & Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
                Author notes
                [* ]Corresponding author: Anna I. Koukkou, email: akukku@ 123456cc.uoi.gr
                [†]

                In memory of professor Constantin Drainas who lost his life in a car accident on July 5th, 2011.

                Article
                Publisher ID: sigs.2265047
                DOI: 10.4056/sigs.2265047
                PMC ID: 3236039
                PubMed ID: 22180818
                SO-VID: bbe4cca2-8d81-40ec-8c3f-fbd8ed14b799
                Copyright statement: Copyright @ 2011
                License:

                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: Pythagoras II
                Funded by: EPEAEK
                Funded by: National Funds
                Funded by: European Social Funds
                Funded by: European Commission FP7 Collaborative Project MICROME
                Award ID: 222886-2
                Funded by: US Department of Energy Office of Science
                Funded by: Biological and Environmental Research Program
                Award ID: DE-AC02-05CH11231
                Award ID: DE-AC52-07NA27344
                Award ID: DE-AC02-06NA25396
                Categories
                Subject: Short Genome Reports

                ScienceOpen disciplines: Genetics
                Keywords: pah biodegradation,mycobacterium gilvum,pyrene degradation
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: pah biodegradation, mycobacterium gilvum, pyrene degradation

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