Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

Standards in Genomic Sciences

Volumn 5, Issue 3, 2011, Pages 269-278

  Grote, Jana ^a,b   Bayindirli, Cansu ^a,c   Bergauer, Kristin ^a,d   de Moraes, Paula Carpintero ^a,e   Chen, Huan ^a,f   D'Ambrosio, Lindsay ^a,g   Edwards, Bethanie ^a,h   Fernández Gómez, Beatriz ^a,i   Hamisi, Mariam ^a,j   Logares, Ramiro ^a,i   Nguyen, Dan ^a,k   Rii, Yoshimi M ^a,l   Saeck, Emily ^a,m   Schutte, Charles ^a,n   Widner, Brittany ^a,o   Church, Matthew J ^a,l   Steward, Grieg F ^a,l   Karl, David M ^a,l   Delong, Edward F ^a,p   Eppley, John M ^p   Schuster, Stephan C ^q   Kyrpides, Nikos C ^r   Rappé, Michael S ^a,b   more..

^a UNIVERSITY OF HAWAII   (United States)

^b UNIVERSITY OF HAWAII   (United States)

^c UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^d UNIVERSITY OF VIENNA   (Austria)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

^f FLORIDA A AND M UNIVERSITY   (United States)

^g University of North Carolina at Chapel Hill   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ Centro Mediterráneo de Investigaciones Marinas y Ambientales   (Spain)

^j UNIVERSITY OF DODOMA   (Tanzania)

^k UNIVERSITÉ DE MONTRÉAL   (Canada)

^l UNIVERSITY OF HAWAII   (United States)

^m GRIFFITH UNIVERSITY   (Australia)

ⁿ UNIVERSITY OF GEORGIA   (United States)

^o Old Dominion University   (United States)

^p Massachusetts Institute of Technology Cambridge   (United States)

^q PENNSYLVANIA STATE UNIVERSITY   (United States)

^r DOE JOINT GENOME INSTITUTE   (United States)

more..

Author keywords

Genome; Marine bacterioplankton; Proteorhodopsin; Rhodospirillaceae; SAR116

Indexed keywords

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); RHODOSPIRILLACEAE;

EID: 84863155147     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1854551     Document Type: Article

References (33)

1. Rappé MS, Brandon ML. Diversity among bacteria from the coastal subtropical Pacific Ocean determined by high-throughput culturing and small-subunit rRNA gene clone libraries. In review.
2. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 1995; 40:148-158.doi:10.4319/lo.1995.40.1.0148
3. Rappé MS, Kemp PF, Giovannoni SJ. Phylogenet-ic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol Oceanogr 1997; 42:811-826.doi:10.4319/lo.1997.42.5.0811
4. Acinas SG, Antón J, Rodríquez-Valera F. Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl Environ Microbiol 1999; 65:514-522.PubMed
5. Rappé MS, Vergin K, Giovannoni SJ. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 2000; 33:219-232.PubMed doi:10.1016/S0168-6496(00)00064-7
6. Giovannoni SJ, Rappé MS. (2000). Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman DL (ed), Microbial Ecology of the Oceans. Wiley and Sons. pp. 47-84.
7. Suzuki MT, Béjà O, Taylor LT, DeLong EF. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 2001; 3:323-331. PubMed doi:10.1046/j.1462-2920.2001.00198.x
8. Giovannoni SJ, Stingl U. Molecular diversity and ecology of microbial plankton. Nature 2005; 437:343-348. PubMed doi:10.1038/nature04158
9. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 2006; 311:496-503. PubMed doi:10.1126/science.1120250
10. Stingl U, Tripp HJ, Giovannoni SJ. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J 2007; 1:361-371. PubMed
11. Oh HM, Kwon KK, Kang I, Kang SG, Lee JH, Kim SJ, Cho JC. Complete genome sequence of "Can-didatus Puniceispirillum marinum": IMCC1322, a representative of the SAR116 clade in the Alpha-proteobacteria. J Bacteriol 2010; 192:3240-3241. PubMed doi:10.1128/JB.00347-10
12. 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 doi:10.1038/nbt1360
13. 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 doi:10.1073/pnas.87.12.4576
14. 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.
15. 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 doi:10.1099/ijs.0.64188-0
16. 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.
17. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. doi:10.1099/00207713-30-1-225
18. Pfennig N, Trüper HG. Higher taxa of the phototrophic bacteria. Int J Syst Bacteriol 1971; 21:17-18. doi:10.1099/00207713-21-1-17
19. 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 doi:10.1038/75556
20. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 2002; 418:630-633. PubMed doi:10.1038/nature00917
21. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241-250. PubMed doi:10.1016/j.syapm.2008.07.001
22. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Kumar Y, Buchner T, Lai S, Steppi G, Jobb W, et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363-1371.PubMed doi:10.1093/nar/gkh293
23. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688-2690.PubMed doi:10.1093/bioinformatics/btl446
24. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758-771.PubMed doi:10.1080/10635150802429642
25. Urios L, Michotey V, Intertaglia L, Lesongeur F, Lebaron P. Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea. Int J Syst Evol Microbiol 2008; 58:2336-2341.PubMed doi:10.1099/ijs.0.64592-0
26. Urios L, Michotey V, Intertaglia L, Lesongeur F, Lebaron P. Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum. Int J Syst Evol Microbiol 2010; 60:209-213.PubMed doi:10.1099/ijs.0.011460-0
27. Zhang GI, Hwang CY, Cho BC. Thalassobaculum litoreum gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from coastal seawater. Int J Syst Evol Microbiol 2008; 58:479-485.PubMed doi:10.1099/ijs.0.65344-0
28. Lai Q, Yuan J, Wu C, Shao Z. Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean. Int J Syst Evol Mi-crobiol 2009; 59:1733-1737.PubMed doi:10.1099/ijs.0.004341-0
29. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119.PubMed doi:10.1186/1471-2105-11-119
30. Markowitz VM, Ivanova NN, Chen A, Chu K, Kyrpides NC. IMG-ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278.PubMed doi:10.1093/bioinformatics/btp393
31. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964.PubMed doi:10.1093/nar/25.5.955
32. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108.PubMed doi:10.1093/nar/gkm160
33. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating noncoding RNAs in complete genomes. Nucleic Acids Res 2004; 33:D121-D124.PubMed doi:10.1093/nar/gki081