ArticlePloS one2010
Mutation detection with next-generation resequencing through a mediator genome.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Improved complete genome sequence ofMicrobiology resource announcements · 2024Article
- Parallel Evolution in PredatoryApplied and environmental microbiology · 2023Article
- Advances in cellular and molecular predatory biology ofFrontiers in microbiology · 2023Review
- Article
- Quantitative Control for Stoichiometric Protein Synthesis.Annual review of microbiology · 2021Article
- To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators.The ISME journal · 2021Article
- Novel Detection of Nasty Bugs, Prevention Is Better than Cure.International journal of molecular sciences · 2020Review
- Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling.PLoS computational biology · 2020Article
- Potential Control of Potato Soft Rot Disease by the Obligate PredatorsApplied and environmental microbiology · 2020Article
- Evolutionary diversification of the RomR protein of the invasive deltaproteobacterium, Bdellovibrio bacteriovorus.Scientific reports · 2019Article
- Shedding Light on the Cell Biology of the Predatory BacteriumFrontiers in microbiology · 2019Article
- Analysis of spontaneous suppressor mutants from the photomixotrophically grown pmgA-disrupted mutant in the cyanobacterium Synechocystis sp. PCC 6803.Photosynthesis research · 2015Article
- Cell-cycle progress in obligate predatory bacteria is dependent upon sequential sensing of prey recognition and prey quality cues.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.PLoS computational biology · 2015Article
- BREX is a novel phage resistance system widespread in microbial genomes.The EMBO journal · 2015Article
- Spatially Organized Films from Bdellovibrio bacteriovorus Prey Lysates.Applied and environmental microbiology · 2014Article
- Next generation genetic mapping of the Ligon-lintless-2 (Li₂) locus in upland cotton (Gossypium hirsutum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Using next-generation sequencing to isolate mutant genes from forward genetic screens.Nature reviews. Genetics · 2014Review
- In and out: an analysis of epibiotic vs periplasmic bacterial predators.The ISME journal · 2014Article
- The lifestyle switch protein Bd0108 of Bdellovibrio bacteriovorus is an intrinsically disordered protein.PloS one · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The affordability of next generation sequencing (NGS) is transforming the field of mutation analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by sequencing the entire genome of the mutant and comparing it to the wild-type (WT) genome, thus identifying acquired mutations. A major limitation for this approach is the need for an a-priori sequenced reference genome for the WT organism, as the short reads of most current NGS approaches usually prohibit de-novo genome assembly. To overcome this limitation we propose a general framework that utilizes the genome of relative organisms as mediators for comparing WT and mutant bacteria. Under this framework, both mutant and WT genomes are sequenced with NGS, and the short sequencing reads are mapped to the mediator genome. Variations between the mutant and the mediator that recur in the WT are ignored, thus pinpointing the differences between the mutant and the WT. To validate this approach we sequenced the genome of Bdellovibrio bacteriovorus 109J, an obligatory bacterial predator, and its prey-independent mutant, and compared both to the mediator species Bdellovibrio bacteriovorus HD100. Although the mutant and the mediator sequences differed in more than 28,000 nucleotide positions, our approach enabled pinpointing the single causative mutation. Experimental validation in 53 additional mutants further established the implicated gene. Our approach extends the applicability of NGS-based mutant analyses beyond the domain of available reference genomes.
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