Open Access

Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037

  • Simon Kelly1,
  • John Sullivan1,
  • Clive Ronson1,
  • Rui Tian2,
  • Lambert Bräu3,
  • Karen Davenport4,
  • Hajnalka Daligault4,
  • Tracy Erkkila4,
  • Lynne Goodwin4,
  • Wei Gu4,
  • Christine Munk4,
  • Hazuki Teshima4,
  • Yan Xu4,
  • Patrick Chain4,
  • Tanja Woyke5,
  • Konstantinos Liolios5,
  • Amrita Pati5,
  • Konstantinos Mavromatis6,
  • Victor Markowitz6,
  • Natalia Ivanova5,
  • Nikos Kyrpides5, 7 and
  • Wayne Reeve2Email author
Standards in Genomic Sciences20149:7

https://doi.org/10.1186/1944-3277-9-7

Received: 13 June 2014

Accepted: 16 June 2014

Published: 8 December 2014

Abstract

Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a Lotus divaricatus root nodule. Compared to most other M. loti strains, it has a broad host range and is one of very few M. loti strains able to form effective nodules on the agriculturally important legume Lotus pedunculatus. NZP2037 is an aerobic, Gram negative, non-spore-forming rod. This report reveals that the genome of M. loti strain NZP2037 does not harbor any plasmids and contains a single scaffold of size 7,462,792 bp which encodes 7,318 protein-coding genes and 70 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Keywords

Root-nodule bacteria Nitrogen fixation Symbiosis Alphaproteobacteria

Introduction

Mesorhizobium loti strain NZP2037 (ICMP1326) was isolated in 1961 from a root nodule off a Lotus divaricatus plant growing near Palmerston North airport, New Zealand [1]. Strain NZP2037 is distinguished from most other strains of M. loti by its broad host range (see below), including the ability to form effective nodules on the agriculturally important legume Lotus pedunculatus (syn. L. uliginosus) [2]. Most M. loti strains, including the type strain NZP2213, are only able to induce uninfected nodule primordia on this host [2, 3].

The ability of M. loti strains to form effective nodules on L. pedunculatus was correlated with their ‘in vitro’ sensitivity to flavolans (condensed tannins) present in high concentration in the roots of this legume [4]. The resistance of M. loti strain NZP2037 to flavolans from L. pedunculatus was associated with the presence of a strain-specific polysaccharide component in the outer cell membrane complex of the bacterium [5]. However the genes required for the synthesis of this flavolan-binding polysaccharide have not been identified and whether the polysaccharide is necessary for nodulation of L. pedunculatus has not been established.

Nodulation and nitrogen fixation genes in Mesorhizobium loti strains are encoded on the chromosome on acquired genetic elements termed symbiosis islands [6]. The sequence of the strain NZP2037 symbiosis island was recently reported and it was found that it was split into two regions of 528 kb and 5 kb as the result of a large-scale genome rearrangement [7]. This observation is confirmed by the whole-genome sequence reported in this paper. The Nod factor produced by NZP2037 contains an extra carbamoyl group at its non-reducing end compared to that produced by most other M. loti strains [8] and the NZP2037 symbiosis island contains a nodU gene that is likely responsible for this modification [7]. The symbiosis island was also found to contain nodFEGA genes absent from M. loti strain R7A that may lead to the incorporation of unsaturated fatty acid moieties on the Nod factor [7]. Whether these genes contribute to the broad host range of strain NZP2037 has not been reported.

The broad host range of NZP2037 was exploited by Hotter and Scott [9] to show that rhizobial exopolysaccharide was required for the formation of infected nodules on the indeterminate host Leucaena leucocephala but not on the determinate nodulating host L. pedunculatus. This observation supported suggestions that acidic EPS is required for effective nodulation of indeterminate but not determinate nodulating legumes (reviewed by [10]). However recent work by Kelly et al. using M. loti strain R7A showed that certain rhizobial exopolysaccharide mutants including exoU mutants induced only uninfected nodules on L. corniculatus, supporting a role for exopolysaccharide in determinate nodulation [11]. Interestingly, exoU mutants of NZP2037 form effective nodules on L. corniculatus [12], again suggesting that NZP2037 may produce a strain-specific surface polysaccharide that plays a symbiotic role.

Here we present a summary classification and a set of general features for M. loti strain NZP2037 together with the description of the complete genome sequence and annotation.

Classification and general features

Mesorhizobium loti strain NZP2037 is in the order Rhizobiales of the class Alphaproteobacteria. Cells are described as non-sporulating, Gram-negative, non-encapsulated, rods. The rod-shaped form varies in size with dimensions of 0.5-0.75 μm in width and 1.25-1.5 μm in length (Figure 1 left and center). They are moderately fast growing, forming 2 mm diameter colonies within 5 days and have a mean generation time of approximately 6 h when grown in TY broth at 28°C [13]. Colonies on G/RDM agar [14] and half strength Lupin Agar (½LA) [15] are opaque, slightly domed, mucoid with smooth margins (Figure 1 right).
Figure 1

Images of Mesorhizobium loti strain NZP2037 using scanning (left) and transmission (center) electron microscopy and the appearance of colony morphology on ½LA (right).

Strains of this organism are able to tolerate a pH range between 4 and 10. Carbon source utilization and fatty acid profiles of M. loti have been described previously [3, 16, 17]. Minimum Information about the Genome Sequence (MIGS) is provided in Table 1.
Table 1

Classification and general features of Mesorhizobium loti strain NZP2037 according to the MIGS recommendations [18, 19]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [19]

Phylum Proteobacteria

TAS [20]

Class Alphaproteobacteria

TAS [21]

Order Rhizobiales

TAS [22, 23]

Family Phyllobacteriaceae

TAS [23, 24]

Genus Mesorhizobium

TAS [16]

Species Mesorhizobium loti

TAS [3]

Strain NZP2037

TAS [3]

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Motile

IDA

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile

NAS

 

Optimum temperature

28°C

NAS

 

Salinity

Unknown

NAS

MIGS-22

Oxygen requirement

Aerobic

TAS [3]

 

Carbon source

Various

TAS [16, 25]

 

Energy source

chemoorganotroph

TAS [16, 25]

MIGS-6

Habitat

Soil, root nodule, host

TAS [3]

MIGS-15

Biotic relationship

Free living, Symbiotic

TAS [3]

MIGS-14

Pathogenicity

None

NAS

 

Biosafety level

1

TAS [26]

 

Isolation

Root nodule of Lotus divaricatus

TAS [27]

MIGS-4

Geographic location

Adjacent Palmerston North Airport, NZ

TAS [1]

MIGS-5

Nodule collection date

1961

TAS [1]

MIGS-4.1

Latitude

-40.1914

TAS [1]

MIGS-4.2

Longitude

175.3701

TAS [1]

MIGS-4.3

Depth

5 cm

IDA

MIGS-4.4

Altitude

46 meters

IDA

Evidence codes – IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [28].

Figure 2 shows the phylogenetic neighborhood of M. loti strain NZP2037 in a 16S rRNA gene sequence based tree. This strain has 99.7% (1,363/1,367 bp) 16S rRNA gene sequence identity to M. loti MAFF303099 (GOLD ID: Gc00040) and 99.6% sequence identity (1,362/1,397 bp) to M. opportunistum WSM2075 (GOLD ID: Gc01853).
Figure 2

Phylogenetic tree showing the relationships of Mesorhizobium. loti NZP2037 with other root nodule bacteria based on aligned sequences of the 16S rRNA gene (1,290 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA [29], version 5. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [30]. Bootstrap analysis [31] with 500 replicates was performed to assess the support of the clusters. Type strains are indicated with a superscript T. Brackets after the strain name contain a DNA database accession number and/or a GOLD ID (beginning with the prefix G) for a sequencing project registered in GOLD [32]. Published genomes are indicated with an asterisk.

Symbiotaxonomy

Like most other M. loti strains including the type strain NZP2213, strain NZP2037 forms effective nodules on Lotus corniculatus, L. tenuis, L. japonicus, L. burttii, L. krylovii, L. filicaulis and L. schoelleri [2, 33]. However, it also forms nitrogen-fixing nodules on several hosts that strain NZP2213 only induces uninfected nodules on. These hosts include Lotus pedunculatus, L. angustissimus, L. subbiflorus, Leuceana leucocephala, Carmichaelia flagelliformis, Ornithopus sativus and Clianthus puniceus [33].

Genome sequencing and annotation information

Genome project history

This organism was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Community Sequencing Program at the U.S. Department of Energy, Joint Genome Institute (JGI) for projects of relevance to agency missions. The genome project is deposited in the Genomes OnLine Database [32] and a high-quality-draft genome sequence in IMG. Sequencing, finishing and annotation were performed by the JGI. A summary of the project information is shown in Table 2.
Table 2

Genome sequencing project information for Mesorhizobium loti NZP2037

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality-draft

MIGS-28

Libraries used

Illumina Standard (short PE) and CLIP (long PE) libraries

MIGS-29

Sequencing platforms

Illumina HiSeq2000 technology

MIGS-31.2

Sequencing coverage

Illumina: 509×

MIGS-30

Assemblers

Velvet version 1.1.05; Allpaths-LG version r39750 phrap, version 4.24

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

Genbank accession

AQZP00000000

 

Genbank Registration Date

September 16, 2013

 

GOLD ID

Gi08826

 

NCBI project ID

81803

 

Database: IMG

2517572076

 

Project relevance

Symbiotic nitrogen fixation, agriculture

Growth conditions and DNA isolation

M. loti strain NZP2037 was grown to mid logarithmic phase in TY rich medium [34] on a gyratory shaker at 28°C at 250 rpm. DNA was isolated from 60 mL of cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [35].

Genome sequencing and assembly

The draft genome of M. loti NZP2037 was generated at the DOE Joint Genome Institute (JGI) using Illumina technology [36]. For this genome, we constructed and sequenced an Illumina short-insert paired-end library with an average insert size of 270 bp which generated 9,401,642 reads and an Illumina long-insert paired-end library with an average insert size of 3047.66 +/- 2184.11 bp which generated 16,067,290 reads totaling 3,820 Mbp of Illumina data. (unpublished, Feng Chen). All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website [37].

The initial draft assembly contained 13 contigs in 6 scaffolds. The initial draft data was assembled with Allpaths, version 39750, and the consensus was computationally shredded into 10 Kbp overlapping fake reads (shreds). The Illumina draft data was also assembled with Velvet [38], version 1.1.05, and the consensus sequences were computationally shredded into 1.5 Kbp overlapping fake reads (shreds). The Illumina draft data was assembled again with Velvet using the shreds from the first Velvet assembly to guide the next assembly. The consensus from the second VELVET assembly was shredded into 1.5 Kbp overlapping fake reads. The fake reads from the Allpaths assembly and both Velvet assemblies and a subset of the Illumina CLIP paired-end reads were assembled using parallel phrap, version 4.24 (High Performance Software, LLC). Possible mis-assemblies were corrected with manual editing in Consed [3841]. Gap closure was accomplished using repeat resolution software (Wei Gu, unpublished), and sequencing of bridging PCR fragments with Sanger technology. The total ("estimated size" for unfinished) size of the genome is 7.5 Mbp and the final assembly is based on 3,820 Mbp of Illumina draft data, which provides an average 509× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [42] as part of the DOE-JGI genome annotation pipeline, followed by a round of manual curation using the JGI GenePrimp pipeline [43]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [44], RNAMMer [45], Rfam [46], TMHMM [47], and SignalP [48]. Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform [49, 50].

Genome properties

The genome is 7,462,792 nucleotides with 62.76% GC content (Table 3 and Figure 3) and is comprised of a single scaffold and no plasmids. From a total of 7,388 genes, 7,318 were protein encoding and 70 RNA-only encoding genes. Within the genome, 286 pseudogenes were also identified. The majority of genes (80.97%) were assigned a putative function while the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 4.
Table 3

Genome statistics for Mesorhizobium loti NZP2037

Attribute

Value

% of total

Genome size (bp)

7,462,792

100.00

DNA coding region (bp)

6,448,323

86.41

DNA G + C content (bp)

4,683,660

62.76

Number of scaffolds

1

 

Number of contigs

5

 

Total genes

7,388

100.00

RNA genes

70

0.95

rRNA operons

1*

 

Protein-coding genes

7,318

99.05

Genes with function prediction

5,982

80.97

Genes assigned to COGs

5,882

79.62

Genes assigned Pfam domains

6,121

82.85

Genes with signal peptides

654

8.85

Genes coding transmembrane proteins

1,735

23.48

*1 copy of 5S, 2 copies of 16S and 1 copy of 23S rRNA genes.

Figure 3

Graphical map of the single scaffold of Mesorhizobium loti NZP2037. From bottom to the top: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Table 4

Number of protein coding genes of Mesorhizobium loti NZP2037 associated with the general COG functional categories

Code

Value

% age

COG category

J

205

3.14

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

603

9.24

Transcription

L

242

3.71

Replication, recombination and repair

B

7

0.11

Chromatin structure and dynamics

D

34

0.52

Cell cycle control, mitosis and meiosis

Y

0

0.00

Nuclear structure

V

82

1.26

Defense mechanisms

T

262

4.01

Signal transduction mechanisms

M

320

4.90

Cell wall/membrane biogenesis

N

51

0.78

Cell motility

Z

2

0.03

Cytoskeleton

W

1

0.02

Extracellular structures

U

142

2.17

Intracellular trafficking and secretion

O

197

3.02

Posttranslational modification, protein turnover, chaperones

C

381

5.84

Energy production conversion

G

624

9.56

Carbohydrate transport and metabolism

E

798

12.22

Amino acid transport metabolism

F

95

1.46

Nucleotide transport and metabolism

H

242

3.71

Coenzyme transport and metabolism

I

275

4.21

Lipid transport and metabolism

P

267

4.09

Inorganic ion transport and metabolism

Q

213

3.26

Secondary metabolite biosynthesis, transport and catabolism

R

811

12.42

General function prediction only

S

675

10.34

Function unknown

-

1,506

20.38

Not in COGS

Conclusion

The M. loti NZP2037 genome consists of a single chromosome of 7.46 Mb predicted to encode 7,388 genes. The sequencing was completed to the stage where a single scaffold comprising 5 contigs was obtained. NZP2037 differs from other well-characterised M. loti strains in that it is able to form effective nodules on the host L. pedunculatus (syn. L. uliginosus) [2]. The molecular basis of this extended host range remains unknown; however NZP2307 carries additional nod genes (nodU, nodFEG and a second copy of nodA) not found in other well-characterised M. loti strains such as MAFF303099 and R7A [7]. Preliminary studies suggest it may also produce some different surface polysaccharides to R7A [11, 12].

Previously it was demonstrated that NZP2037 contains a transmissible plasmid of 240 MDa (approximately 360 kb) designated pRlo22037a [25]. Strain PN4010, a plasmid-cured derivative of NZP2037, showed enhanced levels of nitrogen fixation and competitiveness on Lotus pendunculatus versus the wild-type. Reintroduction of the plasmid into PN4010 returned the strain to the wild-type phenotype [51]. A type IV secretion system consisting of a trb gene cluster (Locus tags 7041-7051 coordinates 70104004-7113626) and traG (locus tag 6995 coordinates 7068484-7070472) highly similar (80-98% amino acid identity) to that of the M. loti strain MAFF303099 pMlb plasmid are located at the end of the scaffold. This finding and comparison of the genome sequence with that of M. loti strains R7A and MAFF303099 suggests that the right end of the single large scaffold may in fact be a large plasmid.

Declarations

Acknowledgements

This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.

Authors’ Affiliations

(1)
Department of Microbiology and Immunology, University of Otago
(2)
Centre for Rhizobium Studies, Murdoch University
(3)
School of Life and Environmental Sciences, Deakin University
(4)
Los Alamos National Laboratory, Bioscience Division
(5)
DOE Joint Genome Institute
(6)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(7)
Department of Biological Sciences, King Abdulaziz University

References

  1. Young JM, Fletcher MJ: International Collection of Micro-organisms from Plants Catalogue. 3rd edition. Landcare Research; 1997. http://scd.landcareresearch.co.nz/Specimen/ICMP_1326 Google Scholar
  2. Pankhurst CE, Craig AS, Jones WT: Effectiveness of Lotus root nodules. 1: morphology and flavolan content of nodules formed on Lotus pedunculatus by fast-growing Lotus rhizobia. J Exp Bot 1979, 30: 1085–93. http://dx.doi.org/10.1093/jxb/30.6.1085 10.1093/jxb/30.6.1085View ArticleGoogle Scholar
  3. 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 10.1099/00207713-32-3-378View ArticleGoogle Scholar
  4. Pankhurst CE, Jones WT: Effectiveness of Lotus root nodules. 2: relationship between root nodule effectiveness and in vitro sensitivity of fast-growing Lotus rhizobia to flavolans. J Exp Bot 1979, 30: 1095–107. http://dx.doi.org/10.1093/jxb/30.6.1095 10.1093/jxb/30.6.1095View ArticleGoogle Scholar
  5. Jones WT, Macdonald PE, Jones SD, Pankhurst CE: Peptidoglycan-bound polysaccharide associated with resistance of Rhizobium loti strain NZP2037 to Lotus pedunculatus root flavolan. J Gen Microbiol 1987, 133: 2617–29.Google Scholar
  6. 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.95.9.5145PubMed CentralView ArticlePubMedGoogle Scholar
  7. Kasai-Maita H, Hirakawa H, Nakamura Y, Kaneko T, Miki K, Maruya J, Okazaki S, Tabata S, Saeki K, Sato S: Commonalities and differences among symbiosis islands of three Mesorhizobium loti strains. Microbes Environ 2013, 28: 275–8. PubMed http://dx.doi.org/10.1264/jsme2.ME12201 10.1264/jsme2.ME12201PubMed CentralView ArticlePubMedGoogle Scholar
  8. Lopez-Lara IM, Van den Berg JDJ, Thomas-Oates JE, Glushka J, Lugtenberg BJJ, Spaink HP: Structural identification of the lipo-chitin oligosaccharide nodulation signals of Rhizobium loti . Mol Microbiol 1995, 15: 627–38. PubMed http://dx.doi.org/10.1111/j.1365–2958.1995.tb02372.x View ArticlePubMedGoogle Scholar
  9. Hotter GS, Scott DB: Exopolysaccharide mutants of Rhizobium loti are fully effective on a determinate nodulating host but are ineffective on an indeterminate nodulating host. J Bacteriol 1991, 173: 851–9. PubMedPubMed CentralPubMedGoogle Scholar
  10. Gage DJ: Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes. Microbiol Mol Biol Rev 2004, 68: 280–300. PubMed http://dx.doi.org/10.1128/MMBR.68.2.280–300.2004 10.1128/MMBR.68.2.280-300.2004PubMed CentralView ArticlePubMedGoogle Scholar
  11. 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-RView ArticlePubMedGoogle Scholar
  12. Kelly SJ: Requirement for Exopolysaccharide in the Mesorhizobium-Lotus Symbiosis. Dunedin: University of Otago; 2012:p.259.Google Scholar
  13. 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.92.19.8985PubMed CentralView ArticlePubMedGoogle Scholar
  14. 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. PubMedPubMed CentralPubMedGoogle Scholar
  15. 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/BF02376781View ArticleGoogle Scholar
  16. 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.Google Scholar
  17. 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 10.1099/00207713-50-2-787View ArticlePubMedGoogle Scholar
  18. 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: 541–7. PubMed http://dx.doi.org/10.1038/nbt1360 10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  19. 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.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  20. Garrity GM, Bell JA, Phylum LT, XIV: Proteobacteria phyl. nov. In Bergey's Manual of Systematic Bacteriology. Volume 2. 2nd edition. Edited by: Garrity GM, Brenner DJ, Krieg NR, Staley JT. New York: Part B, Springer; 2005:p.1.View ArticleGoogle Scholar
  21. Garrity GM, Bell JA, Lilburn T: Class I. Alphaproteobacteria class. In Bergey's Manual of Systematic Bacteriology. 2nd edition. Edited by: Garrity GM, Brenner DJ, Kreig NR, Staley JT. New York: Springer - Verlag; 2005.Google Scholar
  22. Kuykendall LD: Order VI. Rhizobiales ord. nov. In Bergey's Manual of Systematic Bacteriology. 2nd edition. Edited by: Garrity GM, Brenner DJ, Kreig NR, Staley JT. New York: Springer - Verlag; 2005:p.324.Google Scholar
  23. 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 View ArticleGoogle Scholar
  24. Mergaert J, Swings J: Family IV. Phyllobacteriaceae fam. nov. In Bergey's Manual of Systematic Bacteriology. Volume 2. 2nd edition. Edited by: Garrity GM, Brenner DJ, Krieg NR, Staley JT. New York: Part C, Springer; 2005:p.393.Google Scholar
  25. Pankhurst CE, Broughton WJ, Wieneke U: Transfer of an indigenous plasmid of Rhizobium loti to other rhizobia and Agrobacterium tumefaciens . J Gen Microbiol 1983, 129: 2535–43.PubMedGoogle Scholar
  26. Biological Agents: Technical Rules for Biological Agents. TRBA; 466. http://www.baua.de
  27. Crow VL, Jarvis BDW, Greenwood RM: Deoxyribonucleic acid homologies amond acid-producing strains of Rhizobium. Int J Syst Bacteriol 1981, 31: 152–72. http://dx.doi.org/10.1099/00207713–31–2-152 10.1099/00207713-31-2-152View ArticleGoogle Scholar
  28. 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. PubMed http://dx.doi.org/10.1038/75556 10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  29. 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/msr121PubMed CentralView ArticlePubMedGoogle Scholar
  30. Nei M, Kumar S: Molecular Evolution and Phylogenetics. New York: Oxford University Press; 2000.Google Scholar
  31. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39: 783–91. http://dx.doi.org/10.2307/2408678 10.2307/2408678View ArticleGoogle Scholar
  32. 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/gkn240PubMed CentralView ArticlePubMedGoogle Scholar
  33. Pankhurst CE, Hopcroft DH, Jones WT: Comparative morphology and flavolan content of Rhizobium loti induced effective and ineffective root nodules on Lotus species, Leuceana leucocephala, Carmichaelia flagelliformis, Ornithopus sativus , and Clianthus puniceus . Can J Bot 1987, 65: 2676–85. http://dx.doi.org/10.1139/b87–358 10.1139/b87-358View ArticleGoogle Scholar
  34. 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 10.1099/00221287-84-1-188View ArticlePubMedGoogle Scholar
  35. DOE Joint Genome Institute user homepage http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2014/02/JGI-Bacterial-DNA-isolation-CTAB-Protocol-2012.pdf
  36. Bennett S: Solexa Ltd. Pharmacogenomics 2004, 5: 433–8. PubMed http://dx.doi.org/10.1517/14622416.5.4.433 10.1517/14622416.5.4.433View ArticlePubMedGoogle Scholar
  37. DOE Joint Genome Institute http://www.jgi.doe.gov
  38. Zerbino DR: Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protocols Bioinformatics 2010. Chapter 11:Unit 11.5Google Scholar
  39. 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 View ArticlePubMedGoogle Scholar
  40. 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.8.3.175View ArticlePubMedGoogle Scholar
  41. 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.8.3.195View ArticlePubMedGoogle Scholar
  42. 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 http://dx.doi.org/10.1186/1471–2105–11–119 10.1186/1471-2105-11-119PubMed CentralView ArticlePubMedGoogle Scholar
  43. 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: 455–457. PubMed http://dx.doi.org/10.1038/nmeth.1457 10.1038/nmeth.1457View ArticlePubMedGoogle Scholar
  44. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25: 955–64. PubMed http://dx.doi.org/10.1093/nar/25.5.0955 10.1093/nar/25.5.0955PubMed CentralView ArticlePubMedGoogle Scholar
  45. 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/gkm160PubMed CentralView ArticlePubMedGoogle Scholar
  46. 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/gkg006PubMed CentralView ArticlePubMedGoogle Scholar
  47. 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.2000.4315View ArticlePubMedGoogle Scholar
  48. 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.2004.05.028View ArticlePubMedGoogle Scholar
  49. 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: 2271–78. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393 10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar
  50. Genomes IM: (IMG-ER) platform. http://img.jgi.doe.gov/er
  51. Pankhurst CE, Macdonald PE, Reeves JM: Enhanced nitrogen fixation and competitiveness for nodulation of Lotus pedunculatus by a plasmid-cured derivative of Rhizobium loti . J Gen Microbiol 1986, 132: 2321–2328.Google Scholar

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