skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Draft genome of Paraburkholderia caballeronis TNe-841T, a free-living, nitrogen-fixing, tomato plant-associated bacterium

Journal Article · · Standards in Genomic Sciences
 [1];  [1];  [2];  [2];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [4]; ORCiD logo [1]
  1. Inst. Politécnico Nacional, Mexico City (Mexico)
  2. Dept. of Molecular Cell and Developmental Biology, Los Angeles, CA (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Dept. of Molecular Cell and Developmental Biology, Los Angeles, CA (United States); Univ. of California-Los Angeles, Los Angeles, CA (United States)
+ Show Author Affiliations

Paraburkholderia caballeronis is a plant-associated bacterium. Strain TNe-841T was isolated from the rhizosphere of tomato (Solanum lycopersicum L. var. lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was found to effectively nodulate Phaseolus vulgaris L. However, from an analysis of the genome of strain TNe-841T and from repeat inoculation experiments, we found that this strain did not nodulate bean and also lacked nodulation genes, suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G + C content of 67.01%. The sequence includes 6251 protein-coding genes and 87 RNA genes.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1544024
Journal Information:
Standards in Genomic Sciences, Vol. 12, Issue 1; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

References (32)

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia journal November 2013
Shifting the genomic gold standard for the prokaryotic species definition journal October 2009
Real-Time DNA Sequencing from Single Polymerase Molecules journal January 2009
16S ribosomal DNA amplification for phylogenetic study. journal January 1991
Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris journal September 2013
Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia journal December 2013
Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia journal August 2016
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative journal August 2006
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data journal May 2013
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods journal May 2011
Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato journal June 2017
The minimum information about a genome sequence (MIGS) specification journal May 2008
Among-site rate variation and its impact on phylogenetic analyses journal September 1996
Gene Ontology: tool for the unification of biology journal May 2000
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. journal December 1992
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal June 1990
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence journal March 1997
Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. journal February 2017
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
MUSCLE: multiple sequence alignment with high accuracy and high throughput journal March 2004
International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016 journal July 2017
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood journal October 2003
Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species journal December 2014
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities journal January 2007
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes journal May 2010
IMG 4 version of the integrated microbial genomes comparative analysis system journal October 2013
Sphingopyxis jiangsuensis sp. nov. Isolated From the Surface Water of the Yellow Sea journal June 2022
Co-composting of cotton residues with olive mill wastewater: process monitoring and evaluation of the diversity of culturable microbial populations journal September 2021
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass journal February 2020
Dietary palmitic acid promotes a prometastatic memory via Schwann cells journal November 2021
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence journal March 1997
The Tomato Rhizosphere, an Environment Rich in Nitrogen-Fixing Burkholderia Species with Capabilities of Interest for Agriculture and Bioremediation journal June 2007

Cited By (2)

Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens journal February 2019
Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources journal February 2019

Similar Records

The Clavibacter michiganensis subsp. michiganensis-tomato interactome reveals the perception of pathogen by the host and suggests mechanisms of infection
Journal Article · Sun Jan 01 00:00:00 EST 2012 · Journal of Proteome Research · OSTI ID:1544024
+7 more
Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)
Journal Article · Thu Aug 11 00:00:00 EDT 2016 · BMC Genomics · OSTI ID:1544024
+2 more
Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana
Journal Article · Tue Aug 18 00:00:00 EDT 2020 · International Journal of Systematic and Evolutionary Microbiology · OSTI ID:1544024
+3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Genetics & Heredity
Microbiology
Paraburkholderia caballeronis
Tomato plant
Rhizosphere
Nitrogen fixation
Root nodulation