Improved Mobilome Delineation in Fragmented Genomes

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• The mobilome, comprising mobile genetic elements, significantly influences microbial ecology.
• Genomic islands (GIs) are crucial mobile elements integrated into host chromosomes.
• Accurate delineation of mobile elements is vital, yet challenging for incomplete and metagenome-assembled genomes (MAGs) due to fragmentation and potential misbinning.

Purpose of the Study:

• To assess the undercount of GIs in MAGs compared to isolate genomes.
• To enhance the capability of GI detection software for fragmented genomes.
• To improve the characterization of microbial microdiversity within MAGs.

Main Methods:

• Applied the GI-detection software TIGER to 74,561 genomes across 2,473 microbial species, including MAGs and isolate genomes.
• Updated TIGER to TIGER2, incorporating cross-scaffold search for detecting split GIs across fragmented genomic scaffolds or circular replicons.
• Compared GI detection yields and quality between the original TIGER and TIGER2, and between MAGs and isolate genomes.

Main Results:

• A species-normalized deficit of approximately 1.6 GIs per genome was observed in MAGs relative to isolates.
• The updated TIGER2 software doubled GI detection yields by identifying split GIs.
• Split GIs detected by TIGER2 demonstrated comparable quality to single-scaffold GIs, with potential for missing central portions in highly fragmented GIs.

Conclusions:

• Fragmented MAGs lead to an underestimation of GIs, impacting the understanding of microbial mobilomes.
• TIGER2's cross-scaffold search capability significantly improves GI detection in fragmented genomes, crucial for current genomic databases.
• Enhanced GI detection in MAGs via TIGER2 better captures microdiversity, supporting microbiome research, including virus-host interactions and ecological assessments.