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      Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary

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          Abstract

          Acuticoccus yangtzensis JL1095 T is a proteobacterium from a genus belonging to the family Rhodobacteraceae; it was isolated from surface waters of the Yangtze Estuary, China. This strain displays the capability to utilize aromatic and simple carbon compounds. Here, we present the genome sequence, annotations, and features of A. yangtzensis JL1095 T. This strain has a genome size of 5,043,263 bp with a G + C content of 68.63%. The genome contains 4286 protein-coding genes, 56 RNA genes, and 83 pseudo genes. Many of the protein-coding genes were predicted to encode proteins involved in carbon metabolism pathways, such as aromatic degradation and methane metabolism. Notably, a total of 31 genes were predicted to encode form II carbon monoxide dehydrogenases, suggesting potential for carbon monoxide oxidation. The genome analysis helps better understand the major carbon metabolic pathways of this strain and its role in carbon cycling in coastal marine ecosystems.

          Electronic supplementary material

          The online version of this article (10.1186/s40793-017-0295-6) contains supplementary material, which is available to authorized users.

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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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              GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

              J Besemer (2001)
              Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely 83.2% of the translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts in an experimentally validated set of Escherichia coli genes. We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection methods. Accurate translation start prediction, in addition to the refinement of protein sequence N-terminal data, provides the benefit of precise positioning of the sequence region situated upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites can be revealed and analyzed with higher precision. These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed.
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                Author and article information

                Contributors
                Yao Zhang: yaozhang@xmu.edu.cn
                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): 29 December 2017
                Publication date PMC-release: 29 December 2017
                Publication date Collection: 2017
                Volume: 12
                Electronic Location Identifier: 91
                Affiliations
                [1 ]ISNI 0000 0001 2264 7233, GRID grid.12955.3a, State Key Laboratory of Marine Environmental Sciences, , Xiamen University, ; Xiamen, 361102 People’s Republic of China
                [2 ]ISNI 0000 0001 2264 7233, GRID grid.12955.3a, Institute of Marine Microbes and Ecospheres, , Xiamen University, ; Xiamen, 361102 People’s Republic of China
                Article
                Publisher ID: 295
                DOI: 10.1186/s40793-017-0295-6
                PMC ID: 5747140
                SO-VID: ecd7f553-68fe-476e-8ff3-8d51171a4d61
                Copyright © © The Author(s). 2017
                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 July 2017
                Date accepted : 5 December 2017
                Funding
                Funded by: SOA projects
                Award ID: GASI-03-01-02-03
                Award Recipient :
                Funded by: national key research program
                Award ID: 2016YFA0601400
                Award Recipient :
                Funded by: NSFC project
                Award ID: 41422603
                Award ID: 41676125
                Award ID: 91428308
                Award Recipient :
                Categories
                Subject: Short Genome Report
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Genetics
                Keywords: acuticoccus yangtzensis jl1095t,aromatic compounds degradation,methane metabolism,form ii codh,aerobic co oxidation,yangtze estuary
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: acuticoccus yangtzensis jl1095t, aromatic compounds degradation, methane metabolism, form ii codh, aerobic co oxidation, yangtze estuary

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