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      Complete genome of the switchgrass endophyte Enterobacter clocace P101

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          Abstract

          The Enterobacter cloacae complex is genetically very diverse. The increasing number of complete genomic sequences of E. cloacae is helping to determine the exact relationship among members of the complex. E. cloacae P101 is an endophyte of switchgrass ( Panicum virgatum) and is closely related to other E. cloacae strains isolated from plants. The P101 genome consists of a 5,369,929 bp chromosome. The chromosome has 5,164 protein-coding regions, 100 tRNA sequences, and 8 rRNA operons.

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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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            MRBAYES: Bayesian inference of phylogenetic trees.

            J P Huelsenbeck, F Ronquist (2001)
            The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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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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                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 February 2014
                Publication date Collection: 15 June 2014
                Publication date PMC-release: 15 February 2014
                Volume: 9
                Issue: 3
                Pages: 726-734
                Affiliations
                [1 ]Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA
                [2 ]School of Molecular Biosciences, Washington State University, Pullman, WA, USA
                [3 ]Department of Plant Pathology, Washington State University, Pullman, WA, USA
                [4 ]Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
                Author notes
                [* ]Correspondence: Brenda K. Schroeder ( bschroeder@ 123456wsu.edu )
                Article
                Publisher ID: sigs.4808608
                DOI: 10.4056/sigs.4808608
                PMC ID: 4149030
                PubMed ID: 25197457
                SO-VID: 17427e32-f953-4962-b497-57e79dd8208a
                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: Department of Plant Pathology, College of Agricultural, Human and Natural Resource Sciences
                Award ID: PPNS #0625
                Funded by: Agricultural Research Center
                Award ID: WNP00652
                Funded by: Washington State University ADVANCE program
                Award ID: 0810927
                Funded by: National Science Foundation
                Award ID: DUE 0920151
                Award ID: DUE 1161177
                Categories
                Subject: Short Genome Reports

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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