Complete genome sequence of Kosakonia sacchari type strain SP1T

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 1311-1318

  Chen, Mingyue ^a   Zhu, Bo ^a   Lin, Li ^b   Yang, Litao ^b,c   Li, Yangrui ^b,c   An, Qianli ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b Guangxi Academy of Sciences   (China)

^c GUANGXI UNIVERSITY   (China)

Author keywords

Endophyte; Nitrogen fixation; Plant growth promoting bacteria; Sugarcane; _Enterobacter; _Kosakonia

Indexed keywords

RIBOSOME RNA; RNA 16S; TRANSFER RNA; UNTRANSLATED RNA;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; COMPARATIVE STUDY; DNA BASE COMPOSITION; ENTEROBACTERIACEAE; GENE SEQUENCE; GENETIC ASSOCIATION; KOSAKONIA SACCHARI SP1; NEIGHBOR JOINING METHOD; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT-GROWTH PROMOTING BACTERIUM;

EID: 84954177705     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.5779977     Document Type: Article

References (23)

1. Brady C, Cleenwerck I, Venter S, Coutinho T, De Vos P. Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): Proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 2013; 36:309-319. PubMed http://dx.doi.org/10.1016/j.syapm.2013.03.005
2. Zhu B, Zhou Q, Lin L, Hu C, Shen P, Yang L, An Q, Xie G, Li Y. Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.). Int J Syst Evol Microbiol 2013; 63:2577-2582. PubMed http://dx.doi.org/10.1099/ijs.0.045500-0
3. Gu CT, Li CY, Yang LJ, Huo GC. Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough and reclassification of Enterobacter sacchari Zhu et al. as Kosakonia sacchari comb. nov. Int J Syst Evol Microbiol 2014; in press. PubMed
4. Lin L, Li Z, Hu C, Zhang X, Chang S, Yang L, Li Y, An Q. Plant growth-promoting nitrogen-fixing Enterobacteria are in association with sugarcane plants growing in Guangxi, China. Microbes Environ 2012; 27:391-398. PubMed http://dx.doi.org/10.1264/jsme2.ME11275
5. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731-2739. PubMed http://dx.doi.org/10.1093/molbev/msr121
6. Grimont F. Grimont PAD. The genus Enterobacter. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds), The Prokaryotes Volume 6: Proteobacteria: Gamma Subclass, Springer, New York, 2006, pp. 197-214.
7. Hoffmann H, Stindl S, Stumpf A, Mehlen A, Monget D, Heesemann J, Schleifer KH, Roggenkamp A. Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance. Syst Appl Microbiol 2005; 8:206-212. PubMed http://dx.doi.org/10.1016/j.syapm.2004.12.009
8. Zhu B, Chen M, Lin L, Yang L, Li Y, An Q. Genome sequence of Enterobacter sp. strain SP1, an endophytic nitrogen-fixing bacterium isolated from sugarcane. [PubMed]. J Bacteriol 2012; 194:6963-6964. PubMed http://dx.doi.org/10.1128/JB.01933-12
9. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. [PubMed]. J Mol Biol 2004; 340:783-795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028
10. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. [PubMed]. J Mol Biol 2001; 305:567-580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315
11. Lowe TM, Eddy SR. t-RNAscan-SE: a program for improved detection of transfer RNA gene in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed http://dx.doi.org/10.1093/nar/25.5.0955
12. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. [PubMed]. Nucleic Acids Res 2005; 33:5691-5702. PubMed http://dx.doi.org/10.1093/nar/gki866
13. Madhaiyan M, Peng N, Ji L. Complete genome sequence of Enterobacter sp. strain R4-368, an endophytic N-fixing gammaproteobacterium isolated from surface-sterilized roots of Jatropha curcas L. [PubMed]. Genome Announc 2013; 1:e00544-e13. PubMed
14. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. [PubMed]. Stand Genomic Sci 2010; 2:142-148. PubMed http://dx.doi.org/10.4056/sigs.541628
15. Auch AF, Von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. [PubMed]. Stand Genomic Sci 2010; 2:117-134. PubMed http://dx.doi.org/10.4056/sigs.531120
16. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. [PubMed]. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
17. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
18. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Springer, New York, 2005, p. 1.
19. List Editor. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Microbiol 2005; 55:2235-2238. http://dx.doi.org/10.1099/ijs.0.64108-0
20. Williams KP. Kelly DP. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int J Syst Evol Microbiol 2013; 63:2901-2906. PubMed http://dx.doi.org/10.1099/ijs.0.049270-0
21. Garrity GM, Holt JG. Taxonomic Outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 155-166.
22. Judicial Commission. Conservation of the family name Enterobacteriaceae, of the name of the type genus, and designation of the type species OPINION NO. 15. Int Bull Bacteriol Nomencl Taxon 1958; 8:73-74.
23. Skerman VBD. McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225