ArticleFrontiers in bioinformatics2022
Improved Mobilome Delineation in Fragmented Genomes.
Article in Frontiers in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Integrase-On-Demand: bioprospecting integrases for targeted genomic insertion of genetic cargo.Nucleic acids research · 2026Article
- Exploring phage-host interactions inMicrobiology spectrum · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- The TIGER/Islander resource for genomic islands.Microbiology resource announcements · 2025Article
- Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2025Review
- Expansion of the tmRNA sequence database and new tools for search and visualization.NAR genomics and bioinformatics · 2025Article
- Speeding genomic island discovery through systematic design of reference database composition.PloS one · 2024Article
- Whole-Cell MALDI-ToF MS Coupled with Untargeted Metabolomics Facilitates Investigations of Microbial Chemical Interactions.Chembiochem : a European journal of chemical biology · 2023Article
- Biotic countermeasures that rescueFrontiers in microbiology · 2023Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mobilome of a microbe, i.e., its set of mobile elements, has major effects on its ecology, and is important to delineate properly in each genome. This becomes more challenging for incomplete genomes, and even more so for metagenome-assembled genomes (MAGs), where misbinning of scaffolds and other losses can occur. Genomic islands (GIs), which integrate into the host chromosome, are a major component of the mobilome. Our GI-detection software TIGER, unique in its precise mapping of GI termini, was applied to 74,561 genomes from 2,473 microbial species, each species containing at least one MAG and one isolate genome. A species-normalized deficit of ∼1.6 GIs/genome was measured for MAGs relative to isolates. To test whether this undercount was due to the higher fragmentation of MAG genomes, TIGER was updated to enable detection of split GIs whose termini are on separate scaffolds or that wrap around the origin of a circular replicon. This doubled GI yields, and the new split GIs matched the quality of single-scaffold GIs, except that highly fragmented GIs may lack central portions. Cross-scaffold search is an important upgrade to GI detection as fragmented genomes increasingly dominate public databases. TIGER2 better captures MAG microdiversity, recovering niche-defining GIs and supporting microbiome research aims such as virus-host linking and ecological assessment.
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