ArticleNucleic acids research2012
OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 50 citations in OpenAlex.
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- Review
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.Cell host & microbe · 2024Article
- Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria.Microbial genomics · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.bioRxiv : the preprint server for biology · 2024Article
- Active Transposition of Insertion Sequences in Prokaryotes: Insights from the Response ofAntioxidants (Basel, Switzerland) · 2022Review
- Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications inMicrobial genomics · 2022Article
- TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis.mBio · 2021Article
- Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare.G3 (Bethesda, Md.) · 2021Article
- digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes.BMC bioinformatics · 2021Article
- The IS6 family, a clinically important group of insertion sequences including IS26.Mobile DNA · 2021Review
- Genome Plasticity by Insertion Sequences Learned From a Case of Radiation-Resistant BacteriumBioinformatics and biology insights · 2021Article
- Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced byFoods (Basel, Switzerland) · 2020Article
- Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (Applied and environmental microbiology · 2020Article
- Transposable elements contribute to the genome plasticity ofMicrobial genomics · 2020Article
- EvaluatingPeerJ · 2020Article
- Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1.PloS one · 2020Article
- Copy number variation is associated with gene expression change in archaea.Microbial genomics · 2018Article
- The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis.BMC genomics · 2014Article
- Bacterial insertion sequences: their genomic impact and diversity.FEMS microbiology reviews · 2014Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertion sequences (ISs) are simple transposable elements present in most bacterial and archaeal genomes and play an important role in genomic evolution. The recent expansion of sequenced genomes offers the opportunity to study ISs comprehensively, but this requires efficient and accurate tools for IS annotation. We have developed an open-source program called OASIS, or Optimized Annotation System for Insertion Sequences, which automatically annotates ISs within sequenced genomes. OASIS annotations of 1737 bacterial and archaeal genomes offered an unprecedented opportunity to examine IS evolution. At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa. This may indicate differential loss, barriers to exchange and/or insufficient time to equilibrate across clades. The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes >2 Mb. At the finer scale of recently diverged genomes, the proportion of shared IS content falls sharply, suggesting loss and/or emergence of barriers to successful cross-infection occurs rapidly. Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.
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Registered trials
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.