Genome sequence of Coxiella burnetii strain Namibia

We present the whole genome sequence and annotation of the Coxiella burnetii strain Namibia. This strain was isolated from an aborting goat in 1991 in Windhoek, Namibia. The plasmid type QpRS was confirmed in our work. Further genomic typing placed the strain into a unique genomic group. The genome sequence is 2,101,438 bp long and contains 1,979 protein-coding and 51 RNA genes, including one rRNA operon. To overcome the poor yield from cell culture systems, an additional DNA enrichment with whole genome amplification (WGA) methods was applied. We describe a bioinformatics pipeline for improved genome assembly including several filters with a special focus on WGA characteristics.

• Publication year

  2014

• Venue

  Standards in Genomic Sciences

• Publication date

  2014-12-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/1944-3277-9-22PMID 25593636PMCID 4286197
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Legionellales ord. nov.

  2015cited by this paper
• Database resources of the National Center for Biotechnology Information

  2014cited by this paper
• Eight New Genomes and Synthetic Controls Increase the Accessibility of Rapid Melt-MAMA SNP Typing of Coxiella burnetii

  2014cited by this paper
• SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

  2013cited by this paper
• Data, information, knowledge and principle: back to metabolism in KEGG

  2013cited by this paper
• Microevolution of the Chromosomal Region of Acute Disease Antigen A (adaA) in the Query (Q) Fever Agent Coxiella burnetii

  2013cited by this paper
• QUAST: quality assessment tool for genome assemblies

  2013cited by this paper
• Activities at the Universal Protein Resource (UniProt)

  2013cited by this paper
• Whole genome amplification of the obligate intracellular pathogen Coxiella burnetii using multiple displacement amplification.

  2013cited by this paper
• GAM-NGS: genomic assemblies merger for next generation sequencing

  2013cited by this paper
• BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

  2012cited by this paper
• BSL3 and BSL4 agents : epidemiology, microbiology, and practical guidelines

  2012cited by this paper
• BayesHammer: Bayesian clustering for error correction in single-cell sequencing

  2012cited by this paper
• IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

  2012cited by this paper
• Coxiella burnetii: Q Fever

  2012cited by this paper
• Toward almost closed genomes with GapFiller

  2012cited by this paper
• Database resources of the National Center for Biotechnology Information

  2012cited by this paper
• SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

  2012cited by this paper
• Rfam 11.0: 10 years of RNA families

  2012cited by this paper
• COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

  2012cited by this paper
• Cutadapt removes adapter sequences from high-throughput sequencing reads

  2011cited by this paper
• Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7

  2011cited by this paper
• Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

  2011cited by this paper
• Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

  2011cited by this paper
• phangorn: phylogenetic analysis in R

  2010cited by this paper
• Database resources of the National Center for Biotechnology Information

  2009cited by this paper
• Reordering contigs of draft genomes using the Mauve Aligner

  2009cited by this paper
• Standards in Genomic Sciences

  2009cited by this paper
• Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

  2009cited by this paper
• Host cell-free growth of the Q fever bacterium Coxiella burnetii

  2009cited by this paper
• The minimum information about a genome sequence (MIGS) specification

  2008cited by this paper
• Comparative Genomics Reveal Extensive Transposon-Mediated Genomic Plasticity and Diversity among Potential Effector Proteins within the Genus Coxiella

  2008influential reference
• The minimum information about a genome sequence (MIGS) specification

  2008cited by this paper
• PEDANT covers all complete RefSeq genomes

  2008cited by this paper
• Sustained Axenic Metabolic Activity by the Obligate Intracellular Bacterium Coxiella burnetii

  2008cited by this paper
• Mechanism of chimera formation during the Multiple Displacement Amplification reaction

  2007cited by this paper
• Efficient Method of Cloning the Obligate Intracellular Bacterium Coxiella burnetii

  2007cited by this paper
• Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

  2007cited by this paper
• RNAmmer: consistent and rapid annotation of ribosomal RNA genes

  2007cited by this paper
• IS1111 insertion sequences of Coxiella burnetii: characterization and use for repetitive element PCR-based differentiation of Coxiella burnetii isolates

  2007cited by this paper
• Identifying bacterial genes and endosymbiont DNA with Glimmer

  2007cited by this paper
• The Unusual 23S rRNA Gene of Coxiella burnetii: Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG

  2007cited by this paper
• Unsupervised segmentation of continuous genomic data

  2007cited by this paper
• A hybrid microfluidic-vacuum device for direct interfacing with conventional cell culture methods

  2007cited by this paper
• Highly sensitive real-time PCR for specific detection and quantification of Coxiella burnetii

  2006cited by this paper
• Genomic DNA Amplification from a Single Bacterium

  2005cited by this paper
• Conventional viral cultures and shell vial assay for diagnosis of apparently culture-negativeCoxiella burnetii endocarditis

  2005cited by this paper
• Validation of publication of new names and new combinations previously effectively published outside the IJSEM.

  2005cited by this paper
• Coxiella burnetii Genotyping

  2005cited by this paper
• APE: Analyses of Phylogenetics and Evolution in R language

  2004cited by this paper
• Improved prediction of signal peptides: SignalP 3.0.

  2004cited by this paper
• SCOP database in 2004: refinements integrate structure and sequence family data

  2004cited by this paper
• Validation of publication of new names and new combinations previously effectively published outside the IJSEM.

  2003cited by this paper
• The IS1111 Family Members IS4321 and IS5075 Have Subterminal Inverted Repeats and Target the Terminal Inverted Repeats of Tn21 Family Transposons

  2003cited by this paper
• Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH.

  2003cited by this paper
• Coxiella burnetii plasmid types QpDG and QpH1 are closely related and likely identical.

  2002cited by this paper
• GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

  2001cited by this paper
• Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

  2001cited by this paper
• Sequencing and characterization of the cryptic plasmid QpRS from Coxiella burnetii.

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Genome Sequence Assembly Using Trace Signals and Additional Sequence Information

  1999cited by this paper
• Hyperendemic focus of Q fever related to sheep and wind.

  1999cited by this paper
• Q Fever

  1999cited by this paper
• Plasmid-homologous sequences in the chromosome of plasmidless Coxiella burnetii Scurry Q217

  1997cited by this paper
• tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

  1997cited by this paper
• Characterization of the 23S and 5S rRNA genes of Coxiella burnetii and identification of an intervening sequence within the 23S rRNA gene

  1995cited by this paper
• A new plasmid (QpDV) common to Coxiella burnetii isolates associated with acute and chronic Q fever.

  1995cited by this paper
• Analysis of the entire nucleotide sequence of the cryptic plasmid QpH1 fromCoxiella burnetii

  1994cited by this paper
• Is plasmid based differentiation ofCoxiella burnetii in ‘acute’ and ‘chronic’ isolates still valid?

  1994cited by this paper
• Analysis of the entire nucleotide sequence of the cryptic plasmid QpH1 from Coxiella burnetti.

  1994cited by this paper
• Q Fever: The Biology of Coxiella burnetii

  1991cited by this paper
• Basic local alignment search tool.

  1990influential reference
• Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

  1990cited by this paper
• Phylogenetic diversity of the Rickettsiae

  1989cited by this paper
• pH dependence of the Coxiella burnetii glutamate transport system

  1983cited by this paper
• Experimental studies on the virus of "Q" fever.

  1983cited by this paper
• Biochemical stratagem for obligate parasitism of eukaryotic cells by Coxiella burnetii.

  1981cited by this paper
• Approved lists of bacterial names.

  1980cited by this paper
• STAINING RICKETTSIAE IN YOLK-SAC CULTURES.

  1964cited by this paper
• AIRBORNE Q FEVER

  1961cited by this paper
• Studies on Q fever in man.

  1956cited by this paper
• Studies on Q fever in man.

  1956cited by this paper
• THE GROWTH OF COXIELLA BURNETII IN EMBRYONATED EGGS

  1952cited by this paper
• Public Health Weekly Reports for DECEMBER 30, 1938.

  1938cited by this paper
• A filter-passing Infectious Agent isolated from Ticks. I. Isolation from Dermacentor andersoni, Reactions in Animals, and Filtration Experiments.

  1938cited by this paper
• Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification

  year unknowninfluential reference

• Seroprevalence of Coxiella burnetii and potential tick vectors infesting domestic ruminants and community perception of the disease in pastoral areas of south Omo zone, southern Ethiopia

  2024cites this paper
• Hard ticks (Acari: Ixodidae) and tick-borne diseases of sheep and goats in Africa: A review.

  2023cites this paper
• Coxiella burnetii

  2022cites this paper
• The Coxiella burnetii T4SS Effector AnkF Is Important for Intracellular Replication

  2020cites this paper
• Comparison of Coxiella burnetii Excretion between Sheep and Goats Naturally Infected with One Cattle-Associated Genotype

  2020cites this paper
• Current perspectives on the transmission of Q fever: Highlighting the need for a systematic molecular approach for a neglected disease in Africa.

  2019cites this paper
• A comparative evaluation of genome assembly reconciliation tools

  2017cites this paper
• Multiple Substrate Usage of Coxiella burnetii to Feed a Bipartite Metabolic Network

  2017cites this paper
• Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains

  2017cites this paper
• Approaches for in silico finishing of microbial genome sequences

  2017cites this paper
• Nutrition of intracellular bacteria: Investigation of the metabolic networks in Legionella pneumophila and Coxiella burnetii using GC/MS based isotopologue profiling

  2017cites this paper
• The contribution of genomics to the study of Q fever.

  2016cites this paper
• Coxiella burnetii, agent de la fièvre Q

  2016cites this paper
• Objective review of de novo stand‐alone error correction methods for NGS data

  2016cites this paper
• [Not Available].

  2016cites this paper
• From Q Fever to Coxiella burnetii Infection: a Paradigm Change

  2016cites this paper
• Improved Error Correction of NGS Data

  2016cites this paper
• First Draft Genome Sequence of a Human Coxiella burnetii Isolate, Originating from the Largest Q Fever Outbreak Ever Reported, the Netherlands, 2007 to 2010

  2015cites this paper