Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075T

Standards in Genomic Sciences

Volumn 9, Issue 2, 2013, Pages 294-303

  Reeve, Wayne ^a   Nandasena, Kemanthi ^a   Yates, Ron ^a,e   Tiwari, Ravi ^a   O'Hara, Graham ^a   Ninawi, Mohamed ^a   Chertkov, Olga ^b   Goodwin, Lynne ^b,c   Bruce, David ^b   Detter, Chris ^b   Tapia, Roxanne ^b   Han, Shunseng ^b   Woyke, Tanja ^c   Pitluck, Sam ^c   Nolan, Matt ^c   Land, Miriam ^d   Copeland, Alex ^c   Liolios, Konstantinos ^c   Pati, Amrita ^c   Mavromatis, Konstantinos ^c   Markowitz, Victor ^f   Kyrpides, Nikos ^c   Ivanova, Natalia ^c   Meenakshi, Uma ^a   Howieson, John ^a   more..

^a MURDOCH UNIVERSITY   (Australia)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e Department of Agriculture and Food ^*  (Australia)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Alphaproteobacteria; Evolution; Integrative and conjugative elements; Lateral gene transfer; Nitrogen fixation; Root nodule bacteria; Symbiosis

Indexed keywords

RNA 16S;

ARTICLE; GENE MAPPING; GENE REPLICATION; GENE SEQUENCE; GENE TRANSFER; GENOME PROJECT; MESORHIZOBIUM; MESORHIZOBIUM AUSTRALICUM; MOLECULAR GENETICS; MORPHOLOGY; NITROGEN FIXATION; NODULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PROTEIN DATABASE; SCANNING ELECTRON MICROSCOPY; SEQUENCE HOMOLOGY; SYMBIOSIS; TRANSMISSION ELECTRON MICROSCOPY;

ALPHAPROTEOBACTERIA; ASTRAGALUS PELECINUS; MESORHIZOBIUM; MESORHIZOBIUM CICERI; NEGIBACTERIA; PELECINUS;

EID: 84890776067     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.4538264     Document Type: Article

References (39)

1. Howieson JG, Loi A, Carr SJ. Biserrula pelecinus L.-a legume pasture species with potential for acid, duplex soils which is nodulated by unique root-nodule bacteria. Aust J Agric Res 1995; 46:997-1009. [doi:10.1071/AR9950997]
2. Hackney B, Dear B, Crocker G. Biserrula. In: Industries DoP, editor New South Wales 2007. p 1-5.
3. Nandasena KG, O'Hara GW, Tiwari RP, Yates RJ, Kishinevsky BD, Howieson JG. Symbiotic relationships and root nodule ultrastructure of the pasture legume Biserrula pelecinus L.-a new legume in agriculture. Soil Biol Biochem 2004; 36:1309-1317. [doi:10.1016/j.soilbio.2004.04.012]
4. Nandasena KG, O'Hara GW, Tiwari RP, Sezmis E, Howieson JG. In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L. Environ Microbiol 2007; 9:2496-2511. [doi:10.1111/j.1462-2920.2007.01368.x] [pmid:17803775]
5. Nandasena KG, O'Hara GW, Tiwari RP, Howieson JG. Rapid in situ evolution of nodulating strains for Biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant. Appl Environ Microbiol 2006; 72:7365-7367. [doi:10.1128/AEM.00889-06] [pmid:16936054]
6. Nandasena KG, O'Hara GW, Tiwari RP, Willems A, Howieson JG. Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia. Int J Syst Evol Microbiol 2009; 59:2140-2147. [doi:10.1099/ijs.0.005728-0] [pmid:19605705]
7. Howieson JG, Ewing MA, D'antuono MF. Selection for acid tolerance in Rhizobium meliloti. Plant Soil 1988;105:179-188. [doi:10.1007/BF02376781]
8. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen M, Angiuoli SV, 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; 26:541-547. [doi:10.1038/nbt1360] [pmid:18464787]
9. 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. [doi:10.1073/pnas.87.12.4576] [pmid:2112744]
10. 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.
11. Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. In: Garrity GM, Brenner DJ, Kreig NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology. Second ed: New York: Springer-Verlag; 2005.
12. 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. [doi:10.1099/ijs.0.64188-0] [pmid:16403855]
13. Kuykendall LD. Order VI. Rhizobiales ord. nov. In: Garrity GM, Brenner DJ, Kreig NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology. Second ed: New York: Springer-Verlag; 2005. p 324.
14. Mergaert J, Swings J. Family IV. Phyllobacteriaceae In: Garrity GM, Brenner DJ, Kreig NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology. Second ed: New York: Springer-Verlag; 2005. p 393.
15. 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; 47:895-898. [doi:10.1099/00207713-47-3-895]
16. Chen WX, Wang ET, Kuykendall LD. The Proteobacteria. New York: Springer-Verlag; 2005.
17. Agents B. Technical rules for biological agents. TRBA (http://www.baua.de):466.
18. Nandasena KG, O'Hara GW, Tiwari RP, Willlems A, Howieson JG. Mesorhizobium ciceri biovar biserrulae, a novel biovar nodulating the pasture legume Biserrula pelecinus L. Int J Syst Evol Microbiol 2007; 57:1041-1045. [doi:10.1099/ijs.0.64891-0] [pmid:17473255]
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. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. [doi:10.1038/75556] [pmid:10802651]
20. Kumar S, Tamura K, Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 2004; 5:150-163. [doi:10.1093/bib/5.2.150] [pmid:15260895]
21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783-791. [doi:10.2307/2408678]
22. 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-D479. [doi:10.1093/nar/gkm884] [pmid:17981842]
23. Reeve WG, Tiwari RP, Worsley PS, Dilworth MJ, Glenn AR, Howieson JG. Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria. Microbiology 1999; 145:1307-1316. [doi:10.1099/13500872-145-6-1307] [pmid:10411257]
24. DOE Joint Genome Institute. http://my.jgi.doe.gov/general/index.html
25. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433-438. [doi:10.1517/14622416.5.4.433] [pmid:15165179]
26. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376-380;. [doi:10.1038/nature03959] [pmid:16056220]
27. Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Current Protocols in Bioinformatics 2010;Chapter 11:Unit 11 5.
28. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:175-185. [doi:10.1101/gr.8.3.175] [pmid:9521922]
29. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175-185. [doi:10.1101/gr.8.3.175] [pmid:9521921]
30. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195-202. [doi:10.1101/gr.8.3.195] [pmid:9521923]
31. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Valafar HRAH, editor. Proceeding of the 2006 international conference on bioinformatics & computational biology: CSREA Press; 2006. p 141-146.
32. 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. [doi:10.1186/1471-2105-11-119] [pmid:20211023]
33. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. [doi:10.1038/nmeth.1457] [pmid:20436475]
34. 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. [pmid:9023104]
35. 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. [doi:10.1093/nar/gkm160] [pmid:17452365]
36. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003; 31:439-441. [doi:10.1093/nar/gkg006] [pmid:12520045]
37. 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; 305:567-580. [doi:10.1006/jmbi.2000.4315] [pmid:11152613]
38. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: Signal P 3.0. J Mol Biol 2004; 340:783-795. [doi:10.1016/j.jmb.2004.05.028] [pmid:15223320]
39. 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; 25:2271-2278. [doi:10.1093/bioinformatics/btp393] [pmid:19561336]