Genome sequence of Burkholderia mimosarum strain LMG 23256T, a Mimosa pigra microsymbiont from Anso, Taiwan
© The Author(s) 2014
Published: 15 June 2014
Burkholderia mimosarum strain LMG 23256T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256T was isolated from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan. LMG 23256T is highly effective at fixing nitrogen with M. pigra. Here we describe the features of B. mimosarum strain LMG 23256T, together with genome sequence information and its annotation. The 8,410,967 bp high-quality-draft genome is arranged into 268 scaffolds of 270 contigs containing 7,800 protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
Keywordsroot-nodule bacteria nitrogen fixation rhizobia Betaproteobacteria
Members of the versatile genus Burkholderia occupy a wide range of ecological niches and are found in soil, hospital environments, associated with plants either as epiphytes, endophytes or as pathogens and some are endosymbionts in phytopathogenic fungi or plant-associated insects . As several Burkholderia strains are known to exert plant-beneficial and biocontrol effects, and also contribute to adaptation to environmental stresses, there is increased interest in the use of Burkholderia in agriculture [1,2].
In addition to the different groups of rhizobia from the Alphaproteobacteria, a number of Betaproteobacteria belonging to Burkholderia and Cupriavidus are now also known to be present in legume nodules; they are sometimes referred to as betarhizobia [3–5]. Several Burkholderia species have been described from root nodules of different Mimosa species: B. caribensis from M. pudica and M. diplotricha [4,6], B. mimosarum from M. pigra and M. scabrella , B. nodosa from M. bimucronata and M. scabrella , B. phymatum from M. invisa and Machaerium lunatum [6,9] and B. sabiae from M. caesalpiniifolia . Moreover, several Burkholderia strains have been shown to enter into effective symbiosis with their host .
B. mimosarum was described for a collection of isolates obtained from M. pigra in Taiwan, Venezuela and Brazil and one strain from M. scabrella in Brazil . Since its first description, B. mimosarum has also been isolated from M. pigra nodules in China and Australia [12,13], from M. diplotricha in Papua New Guinea  and M. pudica in French Guiana . M. pigra, as well as M. pudica and M. diplotricha, are notoriously invasive species . M. pudica (sensitive plant) is a small South American shrub that has become a pan-tropical weed, while M. pigra (giant sensitive plant, black mimosa, prickly wood weed, catclaw mimosa) is a shrub that thrives in floodplains, swamps and river banks, where it creates dense spiny thickets . M. diplotricha (creeping sensitive plant, nila grass, giant sensitive plant) is a climbing shrub that scrambles up other plants, quickly producing dense growth . The success of these invasive weeds may in part be due to their highly effective symbiotic associations.
B. mimosarum LMG 23256T (=BCRC 17516, CCUG 54296, NBRC 106338, PAS44) originates from nodules of M. pigra in Taiwan. This legume weed is predominantly nodulated by B. mimosarum in Taiwan. Other Taiwanese Mimosa species are nodulated mainly by Cupriavidus taiwanensis and it has therefore been suggested that the Burkholderia strains were introduced to Taiwan, along with the invasive M. pigra from its native South America, where Burkholderia strains have been isolated more frequently from Mimosa sp. than C. taiwanesis [7,19].
Classification and general features of Burkholderia mimosarum strain LMG 23256T according to the MIGS recommendations 
Species Burkholderia mimosarum
Strain LMG 23256T
Soil, root nodule, on host
Free living, symbiotic
Root nodule of Mimosa pigra
Soil collection date
Classification and features
B. mimosarum LMG 23256T was isolated from M. pigra growing in Anso, Taiwan and was able to nodulate its original host with high efficiency , as well as M. pucida and M. diplotricha . LMG 23256T was shown to outcompete other rhizobia to the point of exclusion for the nodulation of the invasive M. pigra, M. pudica and M. diplotricha under flooded conditions. This predominance was negatively affected by increased nitrate levels in the soil, which thus seems to be a factor affecting rhizobial competition .
With regard to other plant growth promoting properties, LMG 23256T displayed no antifungal activity against Fusarium oxysporum f. sp. phaseoli, did not solubilize calcium-, iron- or aluminum phosphates nor reduce acetylene (ARA) on the N-free media containing fructose, lactate or mannitol as sole carbon source .
Genome sequencing and annotation
Genome project history
Genome sequencing project information for Burkholderia mimosarum LMG 23256T.
Improved high-quality draft
One Illumina fragment library
Illumina HiSeq 2000
Velvet version 1.1.04; Allpaths-LG version r39750
Gene calling methods
NCBI project ID
Symbiotic N2 fixation, agriculture
Genome sequencing and assembly
The genome of B. mimosarum strain LMG 23256T was sequenced at the Joint Genome Institute (JGI) using Illumina technology . An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 14,635,038 reads totaling 2,014 Mbp.
Velvet (—v —s 51 —e 71 —i 2 —t 1 —f “-shortPaired -fastq $FASTQ” —o “-ins_length 250 -min_contig_lgth 500”) 10)
wgsim (-e 0 -1 76 -2 76 -r 0 -R 0 -X 0)
Allpaths-LG (PrepareAllpathsInputs:PHRED64=1 PLOIDY=1 FRAGCOVERAGE=125 JUMPCOVERAGE=25 LONGJUMPCOV=50, RunAllpath-sLG: THREADS=8 RUN=stdshredpairs TARGETS=standard VAPIWARNONLY=True OVERWRITE=True).
The final draft assembly contained 270 contigs in 268 scaffolds. The total size of the genome is 8.4 Mbp and the final assembly is based on 2,014 Mbp of Illumina data, which provides an average 240× coverage of the genome.
Genes were identified using Prodigal  as part of the DOE-JGI annotation pipeline . 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. The tRNAScanSE tool  was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA . 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 . Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) platform .
Genome Statistics for B. mimosarum strain LMG 23256T
% of Total
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Number of scaffolds
Number of contigs
Genes with function prediction
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of protein coding genes of B. mimosarum strain LMG 23256T associated with the general COG functional categories.
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production conversion
Carbohydrate transport and metabolism
Amino acid transport metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolite biosynthesis, transport and catabolism
General function prediction only
Not in COGS
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. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University.
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