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      Draft Genome Sequence for the Type Strain of Corynebacterium afermentans LCDC 88-0199 T, Isolated from a Human Blood Culture

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      Author(s): a , b , c ,
      Publication date (Electronic):
      Journal: Genome Announcements
      Publisher: American Society for Microbiology

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          Abstract

          A draft genome for Corynebacterium afermentans LCDC 88-0199 T was investigated. The size of the genome was 2,345,615 bp with an observed G+C content of 64.85%. Annotation revealed 2 rRNA sequences, 54 tRNA genes, and 2,164 coding sequences. Genome coverage was 85× and consisted of 24 contigs with an N 50 of 187,988 bp.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          T. Magoc, S. L. Salzberg (2013)
          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            In Vitro Activity of 22 Antimicrobial Agents against Corynebacterium and Microbacterium Species Referred to the Canadian National Microbiology Laboratory

            Kathryn Bernard, Ana Pacheco (2015)
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              Taxonomic study of Corynebacterium Group ANF-1 strains: Proposal of Corynebacterium afermentans sp. nov. containing the subspecies C. afermentans subsp. afermentans subsp. nov. and C. afermentans subsp. lipophilum subsp. nov.

              P. Riegel, D. DE BRIEL, G Prevost² … (1993)
              We have determined the cell wall composition, guanine-plus-cytosine (G+C) contents of the DNA, rRNA gene restriction patterns, and the levels of DNA-DNA relatedness of 11 strains identified biochemically as Centers for Disease Control (CDC) Corynebacterium group absolute nonfermenter 1 (Corynebacterium group ANF-1). For seven of these strains, growth is abundant on 5% sheep blood agar, which differentiates them from the four other strains, whose growth requires a lipid supplement such as Tween 80. Two of the lipid-requiring strains produced mucoid colonies on 1% Tween 80-supplemented sheep blood agar. All strains possess cell wall component type IV, short-chain mycolic acids, and G+C contents of DNA of 66 to 68 mol% as determined by reverse-phase high-performance liquid chromatography. DNA-relatedness experiments by an S1 nuclease procedure showed that nine of these strains, including two of the lipid-requiring strains, constitute a new genomic species less than 40% related to Corynebacterium species and other coryneform groups. The lipid-requiring strain T18502 exhibited 98% DNA relatedness with another lipid-requiring strain, T88593 (difference in thermal denaturation midpoint [delta Tm] = 2 degrees C) and 71 to 77% similarity with the nonlipophilic strains (delta Tm range of from to 5 degrees C). Conversely, the DNA relatedness between strain LCDC 88199 and the six other nonlipophilic strains ranged from 86 to 100% (delta Tm range of from 1 to 3 degrees C) and was only 73 and 76% with the lipophilic strains T18502 and T88593, respectively (delta Tm, 3 and 4 degrees C). These results indicated that these two cultural types of bacteria constitute two subspecies within the new genomic species.(ABSTRACT TRUNCATED AT 250 WORDS)
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 7 July 2016
                Publication date Collection: Jul-Aug 2016
                Volume: 4
                Issue: 4
                Electronic Location Identifier: e00661-16
                Affiliations
                [a ]Department of Biology, Université de Saint-Boniface, Winnipeg, Canada
                [b ]National Microbiology Laboratory, CSCHAH Site, Public Health Agency of Canada, Winnipeg, Canada
                [c ]Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
                Author notes
                Address correspondence to Kathryn Bernard, kathy.bernard@ 123456phac-aspc.gc.ca .
                Author information
                http://orcid.org/0000-0002-4115-7771
                Article
                Publisher ID: genomeA00661-16
                DOI: 10.1128/genomeA.00661-16
                PMC ID: 4939793
                PubMed ID: 27389276
                SO-VID: 222cb10e-a708-40c5-9363-800ea97c7bae
                Copyright © Copyright © 2016 Bernier and Bernard.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 18 May 2016
                Date accepted : 19 May 2016
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 7, Pages: 2, Words: 1004
                Funding
                This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date July/August 2016

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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