Performing a cross-scaffold search for genomic islands

Gareth Trubl and researchers from Sandia National Laboratories have created a new computer tool called Tiger2 that scans DNA and looks for genomic islands—sections that look different than the surrounding DNA. Genomic islands are important for understanding life, infection, evolution, and more. These sections typically house antibiotic resistant and toxin producing genes as well as new information that sets organisms or viruses apart from their “siblings” or helps them adapt to their environment. Because the regions are unique and can move between organisms and viruses, they are difficult to detect.

The team initially applied Tiger—unique in its precise mapping of genomic islands—to over 74,000 genomes from 2,400 microbial species and measured a species-normalized deficit of about 1.6 genomic islands per genome. To test whether the undercount was due to the higher fragmentation of genomes, the team updated Tiger to enable detection of split genomic islands whose termini are on separate scaffolds. This update doubled genomic island yields, and the new split genomic islands matched the quality of single-scaffold genomic islands.

This ability to perform a cross-scaffold search is an important upgrade to genomic island detection since fragmented genomes increasingly dominate public databases. Tiger2 will aid detection of viruses in metagenomic datasets, offer insights into population microdiversity, and help address questions such as the balance of temperate phages.

This research received Laboratory Directed Research and Development Program support (21-LW-060).

[C.M. Mageeney, G. Trubl, K.P. Williams, Improved Mobilome Delineation in Fragmented Genomes, Front. Bioinform. (2022), doi: 10.3389/fbinf.2022.866850.]