Open Access

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia

  • Robert Walker1,
  • Elizabeth Watkin1,
  • Rui Tian2,
  • Lambert Bräu3,
  • Graham O’Hara2,
  • Lynne Goodwin4,
  • James Han5,
  • Elizabeth Lobos5,
  • Marcel Huntemann5,
  • Amrita Pati5,
  • Tanja Woyke5,
  • Konstantinos Mavromatis5,
  • Victor Markowitz6,
  • Natalia Ivanova5,
  • Nikos Kyrpides5 and
  • Wayne Reeve2Email author
Standards in Genomic Sciences20149:9030551

https://doi.org/10.4056/sigs.5008793

Published: 15 June 2014

Abstract

Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain 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 bacterianitrogen fixationrhizobia Betaproteobacteria

Introduction

Burkholderia spp. are ubiquitous in the environment and are found in nearly all terrestrial and some marine ecosystems. They have adapted to occupy numerous niches and may have saprophytic, parasitic, pathogenic or symbiotic lifestyles [1]. Emerging evidence suggests an ancient and stable symbiosis between Burkholderia and Mimosa genera within South America [2] and between Burkholderia and legumes from the Papilionoideae subfamily in South Africa [3,4]. Despite this, there is very little data regarding the symbiosis between Burkholderia and endemic legumes outside of South America and South Africa.

In Australia, legumes are predominately nodulated by species from the genera Bradyrhizobium, Ensifer, and Rhizobium [5,6]. There are no published genomes or species descriptions of symbiotic Burkholderia spp. isolated in Australia and there is a paucity of information on the interaction between Burkholderia and endemic Australia legumes. Burkholderia sp. WSM2230 was isolated from an effective nitrogen fixing nodule on Kennedia coccinea grown in an acidic soil (pH(CaCl2) 4.8) collected from Karijini National Park, Western Australia. Its symbiotic phenotype was authenticated in glasshouse experiments (Watkin, unpublished). Recently this isolate was revived from long-term storage from frozen glycerol stocks but failed to form nodules on K. coccinea in axenic glasshouse trials (Walker, unpublished). In this regard, it is interesting that the South African microsymbiont B. tuberum STM678T only infrequently forms effective nodules on Macroptilium atropurpureum (Siratro). A recent study [7] revealed that B. tuberum forms effective nodules on Siratro when water levels are reduced and temperature is increased. Unlike B. tuberum STM678T, the annotation of the genome sequence of the laboratory cultured strain of WSM2230 failed to identify nodulation genes and this offers an explanation for the lack of a nodulation phenotype.

Establishing the genomic sequences of Australian Burkholderia will be beneficial to understand the mutualistic interactions occurring between plant and rhizosphere organisms in low-pH soil. WSM2230 was only isolated from Karijini National Park acidic soil (pH(CaCl2) 4.8) and other sites where the soil pH was higher (pH(CaCl2) >7) did not contain any Burkholderia symbionts. In these more alkaline soils, numerous Bradyrhizobium and Rhizobium spp. were instead trapped (Watkin, unpublished). Soil pH is an edaphic variable that controls microbial biogeography [8] and the acid tolerance of Burkholderia has been shown to account for the biogeographical distribution of this genus [9].

The genome of WSM2230 is one of two Australian Burkholderia genomes (the other being that of WSM2232 (GOLD ID Gi08832)) that have now been sequenced through the Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) program. Here we present a preliminary description of the general features of the Burkholderia sp. WSM2230 together with its genome sequence and annotation. The genomes of WSM2232 and WSM2230 will be an important resource to identify the processes enabling such isolates to adapt to the infertile, highly acidic soils that dominate the Australian landscape.

Classification and features

Burkholderia sp. strain WSM2230 is a motile, non-sporulating, non-encapsulated, Gram-negative rod in the order Burkholderiales of the class Betaproteobacteria. The rod-shaped form varies in size with dimensions of 0.5 µm for width and 1.0–2.0 µm for length (Figure 1 Left and Center). It is fast growing, forming colonies within 1–2 days when grown on LB agar [10] devoid of NaCl and within 2–3 days when grown on half strength Lupin Agar (½LA) [11], tryptone-yeast extract agar (TY) [12] or a modified yeast-mannitol agar (YMA) [13] at 28°C. Colonies on ½LA are -opaque, slightly domed and moderately mucoid with smooth margins (Figure 1 Right).
Figure 1.

Images of Burkholderia sp. strain WSM2230 using scanning (Left) and transmission (Center) electron microscopy and the appearance of colony morphology on a solid medium (Right).

Burkholderia sp. WSM2230 can solubilize inorganic phosphate, produces hydroxymate-like siderophores, and can tolerate a pH range of 4.5 – 9.0 (Walker, unpublished). Minimum Information about the Genome Sequence (MIGS) is provided in Table 1. Figure 2 shows the phylogenetic neighborhood of Burkholderia sp. strain WSM2230 in a 16S rRNA sequence based tree. This strain shares 99% (1352/1364 bp) sequence identity to the 16S rRNA gene of the sequenced strain Burkholderia sp. WSM2232 (Gi08831).
Figure 2.

Phylogenetic tree showing the relationship of Burkholderia sp. strain WSM2230 (shown in bold print) to other members of the order Burkholderiales based on aligned sequences of the 16S rRNA gene (1,242 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA [25], version 5. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [26]. Bootstrap analysis [27] 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 [28]. Published genomes are indicated with an asterisk.

Table 1.

Classification and general features of Burkholderia sp. strain WSM2230 according to the MIGS recommendations [14]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [15]

 

Phylum Proteobacteria

TAS [16]

 

Class Betaproteobacteria

TAS [17,18]

 

Order Burkholderiales

TAS [18,19]

 

Family Burkholderiaceae

TAS [18,20]

 

Genus Burkholderia

TAS [2123]

 

Species Burkholderia sp.

IDA

 

Strain WSM2230

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Motile

IDA

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile

IDA

 

Optimum temperature

30°C

IDA

 

Salinity

Non-halophile

IDA

MIGS-22

Oxygen requirement

Aerobic

IDA

 

Carbon source

Varied

IDA

 

Energy source

Chemoorganotroph

NAS

MIGS-6

Habitat

Soil, root nodule, on host

IDA

MIGS-15

Biotic relationship

Free living, symbiotic

IDA

MIGS-14

Pathogenicity

Non-pathogenic

IDA

 

Biosafety level

1

IDA

 

Isolation

Root nodule of Kennedia coccinea

IDA

MIGS-4

Geographic location

Karijini National Park, Australia

IDA

MIGS-5

Soil collection date

September 2001

IDA

MIGS-4.1

Latitude

117.99

IDA

MIGS-4.2

Longitude

-22.5

IDA

MIGS-4.3

Depth

0–10 cm

IDA

MIGS-4.4

Altitude

Not reported

 

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 [24].

Symbiotaxonomy

Burkholderia sp. WSM2230 formed nodules (Nod+) on, and fixed N2 (Fix+) with, K. coccinea when first isolated. However, after long term storage and its subsequent culture, it failed to nodulate Australian legume hosts (Table 2).
Table 2.

Compatibility of WSM2230 with nine legume species for nodulation (Nod) and N2-Fixation (Fix)

Species name

Common name

Growth type

Nod

Fix

Reference

K. coccinea

Coral Vine

Perennial

+1

+1

IDA

Swainsona formosa

Sturts Desert Pea

Annual

IDA

Indigofera trita

Annual

IDA

Acacia acuminata

Jam Wattle

Perennial

IDA

A. paraneura

Weeping Mulga

Perennial

IDA

1result obtained from trapping experiment but the isolate failed to nodulate after long term storage.

IDA: Inferred from Direct Assay from the Gene Ontology project [24].

Genome sequencing and annotation

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 [28] and an improved-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 3.
Table 3.

Genome sequencing project information for Burkholderia sp. WSM2230

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved high-quality draft

MIGS-28

Libraries used

1× Illumina library

MIGS-29

Sequencing platforms

Illumina HiSeq 2000

MIGS-31.2

Sequencing coverage

Illumina: 368×

MIGS-30

Assemblers

Velvet version 1.1.04; Allpaths-LG version r39750

MIGS-32

Gene calling methods

Prodigal 1.4

 

GOLD ID

Gi08831

 

NCBI project ID

165309

 

Database: IMG

2513237151

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and DNA isolation

Burkholderia sp. strain WSM2230 was cultured to mid logarithmic phase in 60 ml of TY rich medium on a gyratory shaker at 28°C [29]. DNA was isolated from the cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [30].

Genome sequencing and assembly

The genome of Burkholderia sp. strain WSM2230 was sequenced at the Joint Genome Institute (JGI) using Illumina technology [31]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 15,498,652 reads totaling 2,324 Mbp.

All general aspects of library construction and sequencing performed at the JGI can be found at the JGI user home [30]. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun, L., Copeland, A. and Han, J., unpublished). The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet [32] (version 1.1.04), (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim (https://github.com/lh3/wgsim), (3) Illumina reads were assembled with simulated read pairs using Allpaths-LG [33] (version r39750). Parameters for assembly steps were: 1) Velvet —v —s 51 —e 71 —i 2 —t 1 —f “-shortPaired -fastq $FASTQ” —o “-ins_length 250 -min_contig_lgth 500”), 2) wgsim (-e 0 -1 76 -2 76 -r 0 -R 0 -X 0), 3) Allpaths-LG (STD_1,project,assembly,fragment,1,200,35,,,inward,0,0 SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0).

The final draft assembly contained 33 contigs in 33 scaffolds. The total size of the genome is 6.3 Mbp and the final assembly is based on 2,324 Mbp of Illumina data, which provides an average 368× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [34] as part of the DOE-JGI annotation pipeline [35], followed by a round of manual curation using the JGI GenePrimp pipeline [36]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. The tRNAScanSE tool [37] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [38]. Other non-coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL [39]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) platform [40,41].

Genome properties

The genome is 6,309,801 nucleotides 63.07% GC content (Table 4) and comprised of 33 scaffolds (Figures 3a,3b,3c and Figure 3d) of 33 contigs. From a total of 5,653 genes, 5,590 were protein encoding and 63 RNA only encoding genes. The majority of genes (83.42%) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 5.
Figure 3a.

Graphical map of WSM2230_A3ACDRAFT_scaffold_0.1 of the genome of Burkholderia sp. strain WSM2230. From bottom to the top of each scaffold: 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.

Figure 3b.

Graphical map of WSM2230_A3ACDRAFT_scaffold__3.4 of the genome of Burkholderia sp. strain WSM2230. From bottom to the top of each scaffold: 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.

Figure 3c.

Graphical map of WSM2230_A3ACDRAFT_scaffold_1.2 of the genome of Burkholderia sp. strain WSM2230. From bottom to the top of each scaffold: 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.

Figure 3d.

Graphical map of WSM2230_A3ACDRAFT_scaffold_2.3 of the genome of Burkholderia sp. strain WSM2230. From bottom to the top of each scaffold: 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.

Genome Statistics for Burkholderia sp. strain WSM2230

Attribute

Value

% of Total

Genome size (bp)

6,309,801

100.00

DNA coding region (bp)

5,480,804

86.86

DNA G+C content (bp)

3,979,790

63.07

Number of scaffolds

33

 

Number of contigs

33

 

Total gene

5,653

100.00

RNA genes

63

1.11

rRNA operons*

1

0.02

Protein-coding genes

5,590

98.89

Genes with function prediction

4,716

83.42

Genes assigned to COGs

4,614

81.62

Genes assigned Pfam domains

4,843

85.67

Genes with signal peptides

571

10.10

Genes with transmembrane helices

1,343

23.76

CRISPR repeats

0

 

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

Table 5.

Number of protein coding genes of Burkholderia sp. strain WSM2230 associated with the general COG functional categories

Code

Value

%age

Description

J

179

3.46

Translation, ribosomal structure and biogenesis

A

2

0.04

RNA processing and modification

K

474

9.17

Transcription

L

141

2.73

Replication, recombination and repair

B

1

0.02

Chromatin structure and dynamics

D

40

0.77

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

47

0.91

Defense mechanisms

T

260

5.03

Signal transduction mechanisms

M

357

6.90

Cell wall/membrane/envelope biogenesis

N

103

1.99

Cell motility

Z

0

0.00

Cytoskeleton

W

2

0.04

Extracellular structures

U

128

2.48

Intracellular trafficking, secretion, and vesicular transport

O

169

3.27

Posttranslational modification, protein turnover, chaperones

C

371

7.17

Energy production and conversion

G

395

7.64

Carbohydrate transport and metabolism

E

496

9.59

Amino acid transport and metabolism

F

95

1.84

Nucleotide transport and metabolism

H

197

3.81

Coenzyme transport and metabolism

I

271

5.24

Lipid transport and metabolism

P

233

4.51

Inorganic ion transport and metabolism

Q

173

3.35

Secondary metabolite biosynthesis, transport and catabolism

R

610

11.80

General function prediction only

S

427

8.26

Function unknown

-

1,039

18.38

Not in COGs

Declarations

Acknowledgements

This work was performed under the auspices of the US Department of Energy’s 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)
School of Biomedical Sciences, Faculty of Health Sciences, Curtin University
(2)
Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University
(3)
School of Life and Environmental Sciences, Deakin University
(4)
Bioscience Division, Los Alamos National Laboratory
(5)
DOE Joint Genome Institute
(6)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory

References

  1. Compant S, Nowak J, Coenye T, Clement C, Barka EA. Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol Rev 2008; 32:607–626. PubMed http://dx.doi.org/10.1111/j.1574-6976.2008.00113.xView ArticlePubMedGoogle Scholar
  2. Bontemps C, Elliott GN, Simon MF. Dos Reis Júnior FB, Gross E, Lawton RC, Neto NE, De Fatima Loureiro M, De Faria SM, Sprent JI and others. Burkholderia species are ancient symbionts of legumes. Mol Ecol 2010; 19:44–52. PubMed http://dx.doi.org/10.111365-294X.2009.04458.XView ArticlePubMedGoogle Scholar
  3. Garau G, Yates RJ, Deiana P, Howieson JG. Novel strains of nodulating Burkholderia have a role in nitrogen fixation with Papilionoid herbaceous legumes adapted to acid, infertile soils. Soil Biol Biochem 2009; 41:125–134. http://dx.doi.org/10.1016/j.soilbio.2008.10.011View ArticleGoogle Scholar
  4. Angus AA, Hirsch AM. Insights into the history of the legume-betaproteobacterial symbiosis. Mol Ecol 2010; 19:28–30. PubMed http://dx.doi.org/10.111365-294X.2009.04459.XView ArticlePubMedGoogle Scholar
  5. Thrall PH, Laine A, Broadhurst LM, Bagnall DJ, Brockwell J. Symbiotic effectiveness of rhizobial mutualists varies in interactions with native Australian legume genera. PLoS ONE 2011; 6:e23545. PubMed http://dx.doi.org/10.1371/journal.pone.0023545PubMed CentralView ArticlePubMedGoogle Scholar
  6. Hoque MS, Broadhurst LM, Thrall PH. Genetic characterisation of root nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia. Int J Syst Evol Microbiol 2011; 61:299–309. PubMed http://dx.doi.org/10.1099/ijs.0.021014-0View ArticlePubMedGoogle Scholar
  7. Angus AA, Lee A, Lum MR, Shehayeb M, Hessabi R, Fujishige NA, Yerrapragada S, Kano S, Song N, Yang P, et al. Nodulation and effective nitrogen fixation of Macroptilium atropurpureum (siratro) by Burkholderia tuberum, a nodulating and plant growth promoting beta-proteobacterium, are influenced by environmental factors. Plant Soil 2013; 369:543–562. http://dx.doi.org/10.1007/s11104-013-1590-7View ArticleGoogle Scholar
  8. Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 2006; 103:626–631. PubMed http://dx.doi.org/10.1073/pnas.0507535103PubMed CentralView ArticlePubMedGoogle Scholar
  9. Stopnisek N, Bodenhausen N, Frey B, Fierer N, Eberl L, Weisskopf L. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations. Environ Microbiol 2013. PubMed http://dx.doi.org/10.1111/14622920.12211
  10. Miller JH. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; 1972.Google Scholar
  11. Howieson JG, Ewing MA, D’antuono MF. Selection for acid tolerance in Rhizobium meliloti. Plant Soil 1988; 105:179–188. http://dx.doi.org/10.1007/BF02376781View ArticleGoogle Scholar
  12. Beringer JE. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 1974; 84:188–198. PubMed http://dx.doi.org/10.1099/00221287-84-1-188PubMedGoogle Scholar
  13. Terpolilli JJ. Why are the symbioses between some genotypes of Sinorhizobium and Medicago suboptimal for N2 fixation? Perth: Murdoch University; 2009. 223 p.Google Scholar
  14. 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. PubMed http://dx.doi.org/10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  15. 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.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  16. 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.View ArticleGoogle Scholar
  17. Garrity GM, Bell JA, Lilburn T. Class II. Betaproteobacteria 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. 575.View ArticleGoogle Scholar
  18. 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
  19. Garrity GM, Bell JA, Lilburn T. Order I. Burkholderiales 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. 575.View ArticleGoogle Scholar
  20. Garrity GM, Bell JA, Lilburn T. Family I. Burkholderiaceae 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. 575.View ArticleGoogle Scholar
  21. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 45. Int J Syst Bacteriol 1993; 43:398–399. http://dx.doi.org/10.1099/00207713-43-2-398
  22. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T, Arakawa M. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 1992; 36:1251–1275. PubMed http://dx.doi.org/10.11348-0421.1992.tb02129.xView ArticlePubMedGoogle Scholar
  23. Gillis M, Van TV, Bardin R, Goor M, Hebbar P, Willems A, Segers P, Kersters K, Heulin T, Fernandez MP. Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 1995; 45:274–289. http://dx.doi.org/10.1099/00207713-45-2-274View ArticleGoogle Scholar
  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. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  25. 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; 28:2731–2739. PubMed http://dx.doi.org/10.1093/molbev/msr121PubMed CentralView ArticlePubMedGoogle Scholar
  26. Nei M, Kumar S. Molecular Evolution and Phylogenetics. New York: Oxford University Press; 2000.Google Scholar
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791. http://dx.doi.org/10.2307/2408678View ArticleGoogle Scholar
  28. 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. PubMed http://dx.doi.org/10.1093/nar/gkm884PubMed CentralView ArticlePubMedGoogle Scholar
  29. 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. PubMed http://dx.doi.org/10.1099/13500872-145-6-1307View ArticlePubMedGoogle Scholar
  30. DOI Joint Genome Institute user home. http://my.jgi.doe.gov/general/index.html.
  31. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433–438. PubMed http://dx.doi.org/10.1517/14622416.5.4.433View ArticlePubMedGoogle Scholar
  32. Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Current Protocols in Bioinformatics 2010;Chapter 11:Unit 11 5.Google Scholar
  33. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 2011; 108:1513–1518. PubMed http://dx.doi.org/10.1073/pnas.1017351108PubMed CentralView ArticlePubMedGoogle Scholar
  34. 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/10.1186/1471-2105-11-119PubMed CentralView ArticlePubMedGoogle Scholar
  35. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 2009; 1:63–67. PubMed http://dx.doi.org/10.4056/sigs.632PubMed CentralView ArticlePubMedGoogle Scholar
  36. 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.1457View ArticlePubMedGoogle Scholar
  37. 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. PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  38. Pruesse E, Quast C, Knittel K. Fuchs BdM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188–7196. PubMed http://dx.doi.org/10.1093/nar/gkm864PubMed CentralView ArticlePubMedGoogle Scholar
  39. INFERNAL. http://infernal.janelia.org
  40. 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. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar
  41. Integrated Microbial Genomes (IMG-ER) platform. http://img.jgi.doe.gov/er

Copyright

© The Author(s) 2014