Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

Abstract

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes

“…Nearly all currently known Acrs can be found in MGE sequences, especially phages, highlighting their use as a CRISPR counter-defense mechanism (3). Therefore, we examined the genomes of both S. schleiferi and S. haemolyticus for integrated MGEs using PHASTER (29) and Islander (30) to identify potential hotspots that might harbor Acrs. We found four predicted MGEs in S. schleiferi strain 5909-02 and eight in the contigs of the S. haemolyticus strain W_75 assembly.…”

Structure Analysis of Genomic Islands Flanked by 5’ and 3’ End of the tRNAGly-CCC Gene in Delftia Acidovorans SPH-1

“…Gly-CCC were determined through Islander [13] , but the flanking DRs that were accurately localized in this research should be more reliable and are slightly different with the results of Islander.…”

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

“…The results of panRGP were compared to other tools on the same reference datasets. We included tools that were found to correctly predict GIs in a recent study : Islandpath-dimob (Bertelli and Brinkman, 2018), SigiCFR (Waack et al, 2006), SigiHMM (Waack et al, 2006), Alien Hunter (Vernikos and Parkhill, 2006), PredictBias (Pundhir et al, 2008), ZislandExplorer (Wei et al, 2017) and IslandViewer4 (Bertelli et al, 2017), which combines results from Islander (Hudson et al, 2014), Islandpath-dimob, SigiHMM and IslandPick (Langille et al, 2008). In addition, three recent tools for GI detection were included in the benchmark: GI-cluster (Lu and Leong, 2018), XenoGI (Bush et al, 2018) and IslandCafe (Jani and Azad, 2019).…”