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      Draft genome sequence of Mycobacterium rufum JS14 T, a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii

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          Abstract

          Mycobacterium rufum JS14 T (=ATCC BAA-1377 T, CIP 109273 T, JCM 16372 T, DSM 45406 T), a type strain of the species Mycobacterium rufum sp. . belonging to the family Mycobacteriaceae, was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Hilo (HI, USA) because it harbors the capability of degrading PAH. Here, we describe the first genome sequence of strain JS14 T, with brief phenotypic characteristics. The genome is composed of 6,176,413 bp with 69.25 % G + C content and contains 5810 protein-coding genes with 54 RNA genes. The genome information on M. rufum JS14 T will provide a better understanding of the complexity of bacterial catabolic pathways for degradation of specific chemicals.

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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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              GeneMark.hmm: new solutions for gene finding.

              A. Lukashin (1998)
              The number of completely sequenced bacterial genomes has been growing fast. There are computer methods available for finding genes but yet there is a need for more accurate algorithms. The GeneMark. hmm algorithm presented here was designed to improve the gene prediction quality in terms of finding exact gene boundaries. The idea was to embed the GeneMark models into naturally derived hidden Markov model framework with gene boundaries modeled as transitions between hidden states. We also used the specially derived ribosome binding site pattern to refine predictions of translation initiation codons. The algorithm was evaluated on several test sets including 10 complete bacterial genomes. It was shown that the new algorithm is significantly more accurate than GeneMark in exact gene prediction. Interestingly, the high gene finding accuracy was observed even in the case when Markov models of order zero, one and two were used. We present the analysis of false positive and false negative predictions with the caution that these categories are not precisely defined if the public database annotation is used as a control.
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                Author and article information

                Contributors
                Jae-Ho Shin:
                ORCID: http://orcid.org/0000-0001-6450-9787
                jhshin@knu.ac.kr
                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): 2 August 2016
                Publication date PMC-release: 2 August 2016
                Publication date Collection: 2016
                Volume: 11
                Electronic Location Identifier: 47
                Affiliations
                [1 ]School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701 Republic of Korea
                [2 ]Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822 USA
                Author information
                http://orcid.org/0000-0001-6450-9787
                Article
                Publisher ID: 167
                DOI: 10.1186/s40793-016-0167-5
                PMC ID: 4969647
                PubMed ID: 27486485
                SO-VID: 724ed15a-b98d-4dba-9df9-c7d23681f16e
                Copyright © © The Author(s). 2016
                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 : 12 June 2015
                Date accepted : 13 July 2016
                Categories
                Subject: Short Genome Report
                Custom metadata
                issue-copyright-statement © The Author(s) 2016

                ScienceOpen disciplines: Genetics
                Keywords: mycobacterium,polycyclic aromatic hydrocarbon,biodegradation
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: mycobacterium, polycyclic aromatic hydrocarbon, biodegradation

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