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. 2022 Apr 11:2:866850.
doi: 10.3389/fbinf.2022.866850. eCollection 2022.

Improved Mobilome Delineation in Fragmented Genomes

Catherine M Mageeney  1 , Gareth Trubl  2 , Kelly P Williams  1
Affiliations

Improved Mobilome Delineation in Fragmented Genomes

Catherine M Mageeney et al. Front Bioinform. .

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.

Keywords: genomic island; metagenome-assembled genome mobile genetic element; metagenomeassembled genome; metagenomics; prophage.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
New TIGER modes. The same circular chromosome with 3 (colored) GIs is shown with a complete (A,B) or fragmented assembly (C). With complete assembly, if the origin of the linearized sequence of the circle is randomly chosen, it will occasionally fall within a GI, splitting the GI (B). Yields are shown for the various TIGER modes. The original mode can only find intact GIs on a single scaffold, while the new modes, CircleOrigin (applied to complete assemblies) and Cross (applied to fragmented assemblies), can additionally find the split islands. Because TIGER focuses on GI-flanking sequences, the Cross-mode call for a multiply split GI (red in panel C) will only include the terminal fragments and exclude middle GI fragments.
FIGURE 2
FIGURE 2
GI yields for MAGs and isolate genomes. TIGER2 was run in (A) intact-only mode or (B) split modes on genomes from 2473 GTDB species containing at least one MAG and one isolate genome, measuring GIs/genome within each species; shown here is the mean of the GI/genome values for all species tested at each size (i.e., genome count) cutoff. Data labels show the numbers of species remaining with each size cutoff.
FIGURE 3
FIGURE 3
TIGER2 GI type breakdowns for composition categories (Intact, Cross and CircleOrigin). (A) All GIs, or (B–D) GIs at three Escherichia loci. Percent change is given for Intact vs. Cross GIs; change for Phage1 counts correlates with change in GI length across the three loci.
See this image and copyright information in PMC

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