Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses

Abstract

Horizontal gene transfer constitutes a powerful and innovative force in evolution, but often little is known about the actual origins of transferred genes. Sequence alignments are generally of limited use in tracking the original donor, since still only a small fraction of the total genetic diversity is thought to be uncovered. Alternatively, approaches based on similarities in the genome specific relative oligonucleotide frequencies do not require alignments. Even though the exact origins of horizontally transferred genes may still not be established using these compositional analyses, it does suggest that compositionally very similar regions are likely to have had a common origin. These analyses have shown that up to a third of large acquired gene clusters that reside in the same genome are compositionally very similar, indicative of a shared origin. This brings us closer to uncovering the original donors of horizontally transferred genes, and could help in elucidating possible regulatory interactions between previously unlinked sequences.

Keywords:

• Genomic Islands
• horizontal gene transfer
• genome signature
• compositional analysis

Acknowledgments

M.W.J.vP. is funded by the Netherlands Organization for Scientific Research (NWO) via a VENI grant. This work was further supported by the BioAssist program of the Netherlands Bioinformatics Centre (NBIC), which is supported by the Netherlands Genomics Initiative (NGI). Erik Roos is gratefully acknowledged for his contribution to the original manuscript discussed here, and Michiel Vos and Jon Bohlin are acknowledged for critically reading the manuscript.