Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T)

Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski J (2012)
Standards in Genomic Sciences 7(2): 284-293.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Rückert, ChristianUniBi ; Albersmeier, AndreasUniBi; Al-Dilaimi, ArwaUniBi; Niehaus, KarstenUniBi; Szczepanowski, RafaelUniBi; Kalinowski, JörnUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie
Centrum für Biotechnologie > Arbeitsgruppe K. Niehaus
Abstract / Bemerkung
Corynebacterium halotolerans Chen et al. 2004 is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia of Bacteria and Archaea project.
Stichworte
mesophilic; halotolerant; Gram-positive; non-motile; aerobic
Erscheinungsjahr
2012
Zeitschriftentitel
Standards in Genomic Sciences
Band
7
Ausgabe
2
Seite(n)
284-293
ISSN
1944-3277
eISSN
1944-3277
Page URI
https://pub.uni-bielefeld.de/record/2551038

Zitieren

Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski J. Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T). Standards in Genomic Sciences. 2012;7(2):284-293.
Rückert, C., Albersmeier, A., Al-Dilaimi, A., Niehaus, K., Szczepanowski, R., & Kalinowski, J. (2012). Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T). Standards in Genomic Sciences, 7(2), 284-293. doi:10.4056/sigs.3236691
Rückert, Christian, Albersmeier, Andreas, Al-Dilaimi, Arwa, Niehaus, Karsten, Szczepanowski, Rafael, and Kalinowski, Jörn. 2012. “Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T)”. Standards in Genomic Sciences 7 (2): 284-293.
Rückert, C., Albersmeier, A., Al-Dilaimi, A., Niehaus, K., Szczepanowski, R., and Kalinowski, J. (2012). Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T). Standards in Genomic Sciences 7, 284-293.
Rückert, C., et al., 2012. Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T). Standards in Genomic Sciences, 7(2), p 284-293.
C. Rückert, et al., “Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T)”, Standards in Genomic Sciences, vol. 7, 2012, pp. 284-293.
Rückert, C., Albersmeier, A., Al-Dilaimi, A., Niehaus, K., Szczepanowski, R., Kalinowski, J.: Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T). Standards in Genomic Sciences. 7, 284-293 (2012).
Rückert, Christian, Albersmeier, Andreas, Al-Dilaimi, Arwa, Niehaus, Karsten, Szczepanowski, Rafael, and Kalinowski, Jörn. “Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093T (= DSM 44683T)”. Standards in Genomic Sciences 7.2 (2012): 284-293.

4 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species.
Oliveira A, Oliveira LC, Aburjaile F, Benevides L, Tiwari S, Jamal SB, Silva A, Figueiredo HCP, Ghosh P, Portela RW, De Carvalho Azevedo VA, Wattam AR., Front Microbiol 8(), 2017
PMID: 29075239
Corynebacteriumpollutisoli sp. nov., isolated from hexachlorocyclohexane-contaminated soil.
Negi V, Singh Y, Schumann P, Lal R., Int J Syst Evol Microbiol 66(9), 2016
PMID: 27267453
Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters.
Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S., Biotechnol J 10(2), 2015
PMID: 25139579
Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)).
Schaffert L, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C., Stand Genomic Sci 8(3), 2013
PMID: 24501635

37 References

Daten bereitgestellt von Europe PubMed Central.

An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa.
Zhi XY, Li WJ, Stackebrandt E., Int. J. Syst. Evol. Microbiol. 59(Pt 3), 2009
PMID: 19244447
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM., Nucleic Acids Res. 37(Database issue), 2008
PMID: 19004872
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19914934
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA., Nature 462(7276), 2009
PMID: 20033048
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023
Assignment of Brevibacterium stationis (ZoBell and Upham 1944) Breed 1953 to the genus Corynebacterium, as Corynebacterium stationis comb. nov., and emended description of the genus Corynebacterium to include isolates that can alkalinize citrate.
Bernard KA, Wiebe D, Burdz T, Reimer A, Ng B, Singh C, Schindle S, Pacheco AL., Int. J. Syst. Evol. Microbiol. 60(Pt 4), 2009
PMID: 19661509
Corynebacterium marinum sp. nov. isolated from coastal sediment.
Du ZJ, Jordan EM, Rooney AP, Chen GJ, Austin B., Int. J. Syst. Evol. Microbiol. 60(Pt 8), 2009
PMID: 19783605
Corynebacterium humireducens sp. nov., an alkaliphilic, humic acid-reducing bacterium isolated from a microbial fuel cell.
Wu CY, Zhuang L, Zhou SG, Li FB, He J., Int. J. Syst. Evol. Microbiol. 61(Pt 4), 2010
PMID: 20495037
Corynebacterium deserti sp. nov., isolated from desert sand.
Zhou Z, Yuan M, Tang R, Chen M, Lin M, Zhang W., Int. J. Syst. Evol. Microbiol. 62(Pt 4), 2011
PMID: 21571935
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction.
Bruno WJ, Socci ND, Halpern AL., Mol. Biol. Evol. 17(1), 2000
PMID: 10666718
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL., J. Mol. Biol. 305(3), 2001
PMID: 11152613
Corynebacterium mooreparkense sp. nov. and Corynebacterium casei sp. nov., isolated from the surface of a smear-ripened cheese.
Brennan NM, Brown R, Goodfellow M, Ward AC, Beresford TP, Simpson PJ, Fox PF, Cogan TM., Int. J. Syst. Evol. Microbiol. 51(Pt 3), 2001
PMID: 11411705
Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis.
Renaud FN, Aubel D, Riegel P, Meugnier H, Bollet C., Int. J. Syst. Evol. Microbiol. 51(Pt 5), 2001
PMID: 11594602
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens.
Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T., Genome Res. 13(7), 2003
PMID: 12840036
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
Eddy SR., BMC Bioinformatics 3(), 2002
PMID: 12095421
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A, Chillingworth T, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Quail MA, Rabbinowitsch E, Rutherford KM, Thomson NR, Unwin L, Whitehead S, Barrell BG, Parkhill J., Nucleic Acids Res. 31(22), 2003
PMID: 14602910
Corynebacterium halotolerans sp. nov., isolated from saline soil in the west of China.
Chen HH, Li WJ, Tang SK, Kroppenstedt RM, Stackebrandt E, Xu LH, Jiang CL., Int. J. Syst. Evol. Microbiol. 54(Pt 3), 2004
PMID: 15143024
Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica).
Collins MD, Hoyles L, Foster G, Falsen E., Int. J. Syst. Evol. Microbiol. 54(Pt 3), 2004
PMID: 15143043
Improved prediction of signal peptides: SignalP 3.0.
Bendtsen JD, Nielsen H, von Heijne G, Brunak S., J. Mol. Biol. 340(4), 2004
PMID: 15223320
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese CR, Kandler O, Wheelis ML., Proc. Natl. Acad. Sci. U.S.A. 87(12), 1990
PMID: 2112744
The Corynebacterium xerosis composite transposon Tn5432 consists of two identical insertion sequences, designated IS1249, flanking the erythromycin resistance gene ermCX.
Tauch A, Kassing F, Kalinowski J, Puhler A., Plasmid 34(2), 1995
PMID: 8559800
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Lowe TM, Eddy SR., Nucleic Acids Res. 25(5), 1997
PMID: 9023104
List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet.
Euzeby JP., Int. J. Syst. Bacteriol. 47(2), 1997
PMID: 9103655
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921
Base-calling of automated sequencer traces using phred. II. Error probabilities.
Ewing B, Green P., Genome Res. 8(3), 1998
PMID: 9521922
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608160
Studies in the Nomenclature and Classification of the Bacteria: II. The Primary Subdivisions of the Schizomycetes.
Buchanan RE., J. Bacteriol. 2(2), 1917
PMID: 16558735
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17090583
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW., Nucleic Acids Res. 35(9), 2007
PMID: 17452365
The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glockner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A., Nat. Biotechnol. 26(5), 2008
PMID: 18464787
The National Center for Biotechnology Information's Protein Clusters Database.
Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18940865
CDD: specific functional annotation with the Conserved Domain Database.
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18984618
Corynebacterium maris sp. nov., a marine bacterium isolated from the mucus of the coral Fungia granulosa.
Ben-Dov E, Ben Yosef DZ, Pavlov V, Kushmaro A., Int. J. Syst. Evol. Microbiol. 59(Pt 10), 2009
PMID: 19622641
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 23408721
PubMed | Europe PMC

Suchen in

Google Scholar