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      Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov.

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          Abstract

          Strain G1 T sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus . This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes.

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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 March 2014
                Publication date Collection: 15 June 2014
                Publication date PMC-release: 15 March 2014
                Volume: 9
                Issue: 3
                Pages: 1031-1045
                Affiliations
                [1 ]URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
                [2 ]IRD, University Montpellier 1, Montpellier, France
                [3 ]King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
                Author notes
                [* ]Correspondence: Fadi Bittar ( fadi.bittar@ 123456univ-amu.fr )
                Article
                Publisher ID: sigs.5189179
                DOI: 10.4056/sigs.5189179
                PMC ID: 4149019
                SO-VID: 1a3f848e-80b2-4a52-ac17-dc77a12f3838
                Copyright © Copyright © retained by original authors
                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: Institut de Recherche pour le Développement
                Funded by: Méditerranée-Infection Foundation
                Funded by: Méditerranée-Infection foundation
                Categories
                Subject: Short Genome Reports

                ScienceOpen disciplines: Genetics
                Keywords: paenibacillus gorillae,genome,culturomics,taxonomo-genomics
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: paenibacillus gorillae, genome, culturomics, taxonomo-genomics

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