Resolving the structural features of genomic islands: A machine learning approach

Abstract

Large inserts of horizontally acquired DNA that contain functionally related genes with limited phylogenetic distribution are often referred to as genomic islands (GIs), and structural definitions of these islands, based on common features, have been proposed. Although a large number of mobile elements fall well within the GI definition, there are several concerns about the structural consensus for GIs: The current GI definition was put forward 10 yr ago when only 12 complete bacterial genomes were available, a large number of GIs deviate from that definition, and in silico predictions assuming a full/partial GI structural model bias the sampling of the GI structural space toward "well-structured" GIs. In this study, the structural features of genomic regions are sampled by a hypothesis-free, bottom-up search, and these are exploited in a machine learning approach with the aim of explicitly quantifying and modeling the contribution of each feature to the GI structure. Performing a whole-genome-based comparative analysis between 37 strains of three different genera and 12 outgroup genomes, 668 genomic regions were sampled and used to train structural GI models. The data show that, overall, GIs from the three different genera fall into distinct, genus-specific structural families. However, decreasing the taxa resolution, by studying GI structures across different genus boundaries, provides models that converge on a fairly similar GI structure, further suggesting that GIs can be seen as a superfamily of mobile elements, with core and variable structural features, rather than a well-defined family.

Statistical analyses of conserved features of genomic islands in bacteria

“…First, GIs have the typical length of 10-200 kb (Vernikos and Parkhill, 2008;Soares et al, 2012). We wanted to know what proportion of them would fall out this range.…”

“…We wanted to know what proportion of them would fall out this range. Second, GIs, particularly those recently inserted, tend to have a distinct composition with the host genome and this feature is generally measured by G+C deviation (Khrustalev and Barkovsky, 2011;Soares et al, 2012;Vernikos and Parkhill, 2008), which is defined as…”

“…Third, transposases and integrases, as mobility genes, could aid the integration of GIs into the hosts (Vernikos and Parkhill, 2008;Soares et al, 2012). Hence, most GIs contain mobility genes and the particular proportion was investigated in this study.…”

Stability of a Pseudomonas putida KT2440 Bacteriophage-Carried Genomic Island and Its Impact on Rhizosphere Fitness

“…Common features of GIs include a sequence composition different from that of the core backbone, their insertion is usually adjacent to RNA genes, often flanked by direct repeats, and they frequently include mobility functions (transposases, integrases, or recombinases) (65). Langille et al (36) described two main bioinformatic approaches for identifying GIs: sequence composition-based and comparative genomics-based methods.…”

Lateral genetic transfer: open issues

“…Approximately 10 per cent of known bacterial genomes harbour one or more integrons (Boucher et al 2007), which appear to be more mobilizable and of broader phyletic distribution than recognized until recently. The presence of transposon or integrase sequences suggests past mobility (Vernikos & Parkhill 2008). A particularly long integrated region (e.g.…”