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      High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

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          Abstract

          Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N 2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).

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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 R 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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              tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

              T. M. Lowe, S. Eddy (1997)
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                Author and article information

                Contributors
                Wayne Reeve: W.Reeve@murdoch.edu.au
                Journal
                Journal ID (nlm-ta): Stand Genomic Sci
                Journal ID (iso-abbrev): Stand Genomic Sci
                Title: Standards in Genomic Sciences
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1944-3277
                Publication date (Electronic): 16 October 2015
                Publication date PMC-release: 16 October 2015
                Publication date Collection: 2015
                Volume: 10
                Electronic Location Identifier: 79
                Affiliations
                [ ]Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
                [ ]DOE Joint Genome Institute, Walnut Creek, CA USA
                [ ]Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
                [ ]Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
                [ ]Department of Agriculture and Food, Western Australia, Australia
                Article
                Publisher ID: 72
                DOI: 10.1186/s40793-015-0072-3
                PMC ID: 4609093
                SO-VID: 6bd42f7e-e529-4cd4-b9c0-e250fb651aca
                Copyright © © De Meyer et al. 2015
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 : 26 November 2014
                Date accepted : 8 October 2015
                Categories
                Subject: Short Genome Report
                Custom metadata
                issue-copyright-statement © The Author(s) 2015

                ScienceOpen disciplines: Genetics
                Keywords: root-nodule bacteria,nitrogen fixation,rhizobia,betaproteobacteria,geba-rnb
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: root-nodule bacteria, nitrogen fixation, rhizobia, betaproteobacteria, geba-rnb

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