Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A

Standards in Genomic Sciences

Volumn 9, Issue 1, 2014, Pages

  Kelly, Simon ^a   Sullivan, John ^a   Ronson, Clive ^a   Tian, Rui ^b   Bräu, Lambert ^c   Munk, Christine ^d   Goodwin, Lynne ^d   Han, Cliff ^d   Woyke, Tanja ^e   Reddy, Tatiparthi ^e   Huntemann, Marcel ^e   Pati, Amrita ^e   Mavromatis, Konstantinos ^f   Markowitz, Victor ^f   Ivanova, Natalia ^e   Kyrpides, Nikos ^e,g   Reeve, Wayne ^b  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b MURDOCH UNIVERSITY   (Australia)

^c DEAKIN UNIVERSITY   (Australia)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

^e DOE JOINT GENOME INSTITUTE   (United States)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^g KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Alphaproteobacteria; Nitrogen fixation; Root nodule bacteria; Symbiosis

Indexed keywords

ARCHAEON; GENETIC POLYMORPHISM; GENOME; JOINT; LEGUME; LOTUS JAPONICUS; MESORHIZOBIUM; MICROORGANISM; NITROGEN FIXATION; PLANT MODEL; PLASMID; RHIZOBIACEAE; SYMBIOSIS;

EID: 84971223672     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/1944-3277-9-6     Document Type: Article

References (45)

1. Sullivan JT, Patrick HN, Lowther WL, Scott DB, Ronson CW: Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proc Natl Acad Sci U S A 1995, 92: 8985-9. PubMed http://dx.doi.org/10.1073/pnas.92.19.8985 10.1073/pnas.92.19.8985
2. Jarvis BDW, Pankhurst CE, Patel JJ: Rhizobium loti, a new species of legume root nodule bacteria. Int J Syst Bacteriol 1982, 32: 378-80. http://dx.doi.org/10.1099/00207713-32-3-378 10.1099/00207713-32-3-378
3. Sullivan JT, Ronson CW: Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci U S A 1998, 95: 5145-9. PubMed http://dx.doi.org/10.1073/pnas.95.9.5145 10.1073/pnas.95.9.5145
4. Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS, Weaver JE, Webby RJ, de Bruijn FJ, Ronson CW: Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 2002, 184: 3086-95. PubMed http://dx.doi.org/10.1128/JB.184.11.3086-3095.2002 10.1128/JB.184.11.3086-3095.2002
5. Ramsay JP, Sullivan JT, Stuart GS, Lamont IL, Ronson CW: Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol Microbiol 2006, 62: 723-34. PubMed http://dx.doi.org/10.1111/j.1365-2958.2006.05396.x 10.1111/j.1365-2958.2006.05396.x
6. Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, Sugimoto M, Takeuchi C, Yamada M, Tabata S: Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 2000, 7: 331-8. PubMed http://dx.doi.org/10.1093/dnares/7.6.331 10.1093/dnares/7.6.331
7. Hubber A, Vergunst AC, Sullivan JT, Hooykaas PJJ, Ronson CW: Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system. Mol Microbiol 2004, 54: 561-74. 10.1111/j.1365-2958.2004.04292.x
8. Rodpothong P, Sullivan JT, Songsrirote K, Sumpton D, Cheung KWJT, Thomas-Oates J, Radutoiu S, Stougaard J, Ronson CW: Nodulation gene mutants of Mesorhizobium loti R7A - nodZ and nolL mutants have host-specific phenotypes on Lotus spp. Mol Plant Microbe Interact 2009, 22: 1546-54. PubMed http://dx.doi.org/10.1094/MPMI-22-12-1546 10.1094/MPMI-22-12-1546
9. Kelly SJ, Muszynski A, Kawaharada Y, Hubber AM, Sullivan JT, Sandal N, Carlson RW, Stougaard J, Ronson CW: Conditional requirement for exopolysaccharide in the Mesorhizobium-Lotus symbiosis. Mol Plant Microbe Interact 2013, 26: 319-29. PubMed http://dx.doi.org/10.1094/MPMI-09-12-0227-R 10.1094/MPMI-09-12-0227-R
10. Sullivan JT, Brown SD, Ronson CW: The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator. PLoS One 2013,8(1):e53762. PubMed 10.1371/journal.pone.0053762
11. Ramsay JP, Major AS, Komarovsky VM, Sullivan JT, Dy RL, Hynes MF, Salmond GPC, Ronson CW: A widely conserved molecular switch controls quorum sensing and symbiosis island transfer in Mesorhizobium loti through expression of a novel antiactivator. Mol Microbiol 2013, 87: 1-13. PubMed http://dx.doi.org/10.1111/mmi.12079 10.1111/mmi.12079
12. Ronson CW, Nixon BT, Albright LM, Ausubel FM: Rhizobium meliloti ntrA ( rpoN ) gene is required for diverse metabolic functions. J Bacteriol 1987, 169: 2424-31. PubMed
13. Howieson JG, Ewing MA, D'antuono MF: Selection for acid tolerance in Rhizobium meliloti. Plant Soil 1988, 105: 179-88. http://dx.doi.org/10.1007/BF02376781 10.1007/BF02376781
14. Jarvis BDW, Van Berkum P, Chen WX, Nour SM, Fernandez MP, Cleyet-Marel JC, Gillis M: Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, Rhizobium tianshanense to Mesorhizobium gen.nov. Int J Syst Evol Microbiol 1997, 47: 895-8.
15. Tighe SW, de Lajudie P, Dipietro K, Lindstrom K, Nick G, Jarvis BDW: Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 2000, 50: 787-801. PubMed http://dx.doi.org/10.1099/00207713-50-2-787 10.1099/00207713-50-2-787
16. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen M, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore JL, Cochrane G, Cole J, Dawyndt P, de Vos P, de Pamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, et al.: Towards a richer description of our complete collection of genomes and metagenomes "Minimum Information about a Genome Sequence" (MIGS) specification. Nat Biotechnol 2008, 26: 541-7. PubMed http://dx.doi.org/10.1038/nbt1360 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 U S A 1990, 87: 4576-9. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576 10.1073/pnas.87.12.4576
18. Garrity GM, Bell JA, Lilburn T, Phylum XIV: Proteobacteria phyl. nov. In Bergey's Manual of Systematic Bacteriology. Second Edition, Volume 2, Part B edition. Edited by: Garrity GM, Brenner DJ, Krieg NR, Staley JT. New York: Springer; 2005:1.
19. Garrity GM, Bell JA, Lilburn T: Class I. Alphaproteobacteria class. In Bergey's Manual of Systematic Bacteriology. Second edition. Edited by: Garrity GM, Brenner DJ, Kreig NR, Staley JT. New York: Springer - Verlag; 2005.
20. Kuykendall LD: Order VI. Rhizobiales ord. nov. In Bergey's Manual of Systematic Bacteriology. Second edition. Edited by: Garrity GM, Brenner DJ, Kreig NR, Staley JT. New York: Springer - Verlag; 2005:324.
21. 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
22. Mergaert J, Swings J, Family IV: Phyllobacteriaceae. In Bergy's Manual of Systematic Bacteriology. Second edition. Edited by: Garrity GM, Brenner DJ, Kreig NR, Staley JT. New York: Springer - Verlag; 2005:393.
23. Jarvis BDW, Van Berkum P, Chen XW, Nour SM, Fernandez MP, Cleyet-Marel JC, Gillis M: Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum and Rhizobium tianshanense to Mesorhizobium gen. nov. Int J Syst Bacteriol 1997, 47: 895-8. http://dx.doi.org/10.1099/00207713-47-3-895 10.1099/00207713-47-3-895
24. Biological Agents: Technical rules for biological agents. TRBA.466. http://www.baua.de
25. 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: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25-9. PubMed http://dx.doi.org/10.1038/75556 10.1038/75556
26. 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: 2731-9. PubMed http://dx.doi.org/10.1093/molbev/msr121 10.1093/molbev/msr121
27. Nei M, Kumar S: Molecular Evolution and Phylogenetics. New York: Oxford University Press; 2000.
28. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39: 783-91. http://dx.doi.org/10.2307/2408678 10.2307/2408678
29. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC: The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008, 36: D475-9. PubMed http://dx.doi.org/10.1093/nar/gkm884 10.1093/nar/gkn240
30. Beringer JE: R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 1974, 84: 188-98. PubMed http://dx.doi.org/10.1099/00221287-84-1-188 10.1099/00221287-84-1-188
31. DOE Joint Genome Institute user homepage. http://my.jgi.doe.gov/general/index.html
32. Bennett S, Solexa L: Pharmacogenomics. 2004, 5: 433-8. PubMed http://dx.doi.org/10.1517/14622416.5.4.433 10.1517/14622416.5.4.433
33. DOE Joint Genome Institute. http://www.jgi.doe.gov/
34. Zerbino DR: Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 2010, Chapter 11: 11-5.
35. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8: 186-94. PubMed http://dx.doi.org/10.1101/gr.8.3.175
36. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8: 175-85. PubMed http://dx.doi.org/10.1101/gr.8.3.175 10.1101/gr.8.3.175
37. Gordon D, Abajian C, Green P: Consed: a graphical tool for sequence finishing. Genome Res 1998, 8: 195-202. PubMed http://dx.doi.org/10.1101/gr.8.3.195 10.1101/gr.8.3.195
38. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. Bioinformatics 2010, 11: 119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
39. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC: GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010, 7: 455-7. PubMed http://dx.doi.org/10.1038/nmeth.1457 10.1038/nmeth.1457
40. 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 http://dx.doi.org/10.1093/nar/25.5.0955 10.1093/nar/25.5.0955
41. 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: 3100-8. PubMed http://dx.doi.org/10.1093/nar/gkm160 10.1093/nar/gkm160
42. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR: Rfam: an RNA family database. Nucleic Acids Res 2003, 31: 439-41. PubMed http://dx.doi.org/10.1093/nar/gkg006 10.1093/nar/gkg006
43. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305: 567-80. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315 10.1006/jmbi.2000.4315
44. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340: 783-95. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028 10.1016/j.jmb.2004.05.028
45. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC: IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009, 25: 2271-8. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393 10.1093/bioinformatics/btp393