ArticleGenome research2011
Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
64 citing papers in PubMed, 94 citations in OpenAlex.
- Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.Scientific reports · 2017Trial
- Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.Science (New York, N.Y.) · 2015Trial
- Establishment of titration-based control of DNA replication inScience advances · 2026Article
- Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome.Nature communications · 2026Article
- Evolutionary constraints on RNA polymerase gene positioning in the genome of fast-growing bacteria.Nucleic acids research · 2026Article
- Termination of DNA replication drives genomic instability via multiple mechanisms.Nucleic acids research · 2026Article
- Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events.Molecular biology and evolution · 2025Article
- Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.Phenomics (Cham, Switzerland) · 2025Article
- An additional replication origin causes cell cycle specific DNA replication fork speed.Frontiers in microbiology · 2025Article
- Article
- Chromosomal integrons are genetically and functionally isolated units of genomes.Nucleic acids research · 2024Article
- Bacterial growth dynamics in a rhythmic symbiosis.Molecular biology of the cell · 2024Article
- Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems.Science advances · 2024Article
- Assessing spacer acquisition rates inFrontiers in microbiology · 2024Article
- Interplay between chromosomal architecture and termination of DNA replication in bacteria.Frontiers in microbiology · 2023Review
- The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity.Frontiers in microbiology · 2023Article
- Article
- DNA read count calibration for single-molecule, long-read sequencing.Scientific reports · 2022Article
- Replication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes.Genome biology and evolution · 2022Article
- Deciphering Active Prophages from Metagenomes.mSystems · 2022Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing (WGS) with new short-read sequencing technologies has recently been applied for genome-wide identification of mutations. Genomic rearrangements have, however, often remained undetected by WGS, and additional analyses are required for their detection. Here, we have applied a combination of WGS and genome copy number analysis, for the identification of mutations that suppress the growth deficiency imposed by excessive initiations from the Escherichia coli origin of replication, oriC. The E. coli chromosome, like the majority of bacterial chromosomes, is circular, and DNA replication is initiated by assembling two replication complexes at the origin, oriC. These complexes then replicate the chromosome bidirectionally toward the terminus, ter. In a population of growing cells, this results in a copy number gradient, so that origin-proximal sequences are more frequent than origin-distal sequences. Major rearrangements in the chromosome are, therefore, readily identified by changes in copy number, i.e., certain sequences become over- or under-represented. Of the eight mutations analyzed in detail here, six were found to affect a single gene only, one was a large chromosomal inversion, and one was a large chromosomal duplication. The latter two mutations could not be detected solely by WGS, validating the present approach for identification of genomic rearrangements. We further suggest the use of copy number analysis in combination with WGS for validation of newly assembled bacterial chromosomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.