Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43T)

Standards in Genomic Sciences

Volumn 7, Issue 3, 2013, Pages 440-448

  Fiebig, Anne ^a   Pradella, Silke ^a   Petersen, Jörn ^a   Michael, Victoria ^a   Päuker, Orsola ^a   Rohde, Manfred ^a   Göker, Markus ^a   Klenk, Hans Peter ^a   Wagner Döbler, Irene ^b  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

Aerobic; Bacteriochlorophyll a; Dinoflagellates; Motile; Phenotype microarray; Photoheterotroph; Phyllobacteriaceae; Prorocentrum lima; Rod shaped; Symbiosis

Indexed keywords

RNA 16S;

ALPHAPROTEOBACTERIA; ARTICLE; CHEMOTAXONOMY; DNA EXTRACTION; GENE; GENE SEQUENCE; GENOME; GROWTH; HOEFLEA PHOTOTROPHICA; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOSYNTHESIS; PHYSIOLOGY; PROTEIN ASSEMBLY; PUFL GENE; PUFM GENE; RNA ANALYSIS;

BACTERIA (MICROORGANISMS); DINOPHYCEAE; HOEFLEA PHOTOTROPHICA; PHYLLOBACTERIACEAE; PROROCENTRUM LIMA; RHIZOBIALES;

EID: 84875392801     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3486982     Document Type: Article

References (32)

1. Biebl H, Tindall BJ, Pukall R, Lünsdorf H, Allgaier M, Wagner-Döbler I. Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a. Int J Syst Evol Microbiol 2006; 56:821-826. PubMed http://dx.doi.org/10.1099/ijs.0.63958-0
2. Peix A, Rivas R, Trujillo ME, Vancanneyt M, Velazquez E, Willems A. Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Int J Syst Evol Microbiol 2005; 55:1163-1166. PubMed http://dx.doi.org/10.1099/ijs.0.63291-0
3. Sorokina AI, Chernousova EI, Dubinina GA. Hoeflea siderophila sp. nov., new neutrophilic iron-oxidizing bacteria. Mikrobiologiia 2012; 81:64-71. PubMed
4. Pradella S, Allgaier M, Hoch C, Päuker O, Stackebrandt E, Wagner-Döbler I. Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol 2004; 70:3360-3369. PubMed http://dx.doi.org/10.1128/AEM.70.6.3360-3369.2004
5. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebastopol, 2003.
6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
7. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed http://dx.doi.org/10.1128/AEM.03006-05
8. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
9. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
10. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
11. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
12. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
13. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184-200. http://dx.doi.org/10.1007/978-3-642-02008-7_13
14. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
15. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed http://dx.doi.org/10.1093/nar/gkr1100
16. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
18. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: DJ Brenner, NR Krieg, JT Staley, GM Garrity (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 1.
19. Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 1.
20. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1-6. PubMed http://dx.doi.org/10.1099/ijs.0.64188-0
21. Kuykendall LD. Order VI. Rhizobiales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 324.
22. Mergaert J, Swings J. Family IV. Phyllobacteriaceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 393.
23. BAuA. 2012-update, Classification of Bacteria and Archaea in risk groups. http://www.baua.de TRBA 466, p. 104.
24. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
25. Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 2012; 7:e34846. PubMed http://dx.doi.org/10.1371/journal.pone.0034846
26. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. [doi:10.1089/bio.2010.0029]. Biopreserv Biobank 2011; 9:51-55.
27. Phrap and Phred for Windows, MacOS, Linux, and Unix. www.phrap.com
28. Markowitz VM, Mavromatis K, Ivanova NN, Chen IA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
29. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
30. Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 2007; 35:3100-3108. PubMed http://dx.doi.org/10.1093/nar/gkm160
31. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: Inference of RNA alignments. Bioinformatics 2009; 25:1335-1337. PubMed http://dx.doi.org/10.1093/bioinformatics/btp157
32. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944-945. PubMed http://dx.doi.org/10.1093/bioinformatics/16.10.944