Connecting genomic islands across prokaryotic and phage genomes via protein families

Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.

Automated summary

Prokaryotic genomes evolve through horizontal gene transfer, mutations, and rearrangements. Genomic islands (GIs) play an important role in the horizontal gene transfer process. Previous research in computational biology has focused on developing tools to detect GIs in prokaryotic genomes, but little is known about GI patterns and biological connections across species. In this study, we connected GIs across prokaryotic and phage genomes using patterns of protein families, which led to the discovery of broad HGT connections across the bacterial kingdom and its associated phages.