Abstract
BackgroundGenomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes.ResultsSWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za, was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface.ConclusionsSWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.
Highlights
Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT)
Prediction of genomic islands in eukaryotic chromosomes using SeqWord Gene Island Sniffer (SWGIS) v2.0 The basic principle behind the SWGIS algorithm consisted in a superimposition of values of several statistical parameters calculated for a sliding window
We reported the first estimates for predicting false positive and false negative GIs for a parametric GI search tool tested on eukaryotes
Summary
Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Horizontal gene transfer (HGT) allows organisms to rapidly adapt to fluctuating environments and different ecological pressures or opportunities [3, 4]. There is, compelling examples in some eukaryotic species of where HGT allowed ecological niche speciality [7, 8], drove metabolic innovation and expansion [9, 10] and accelerated the adaptation to completely novel lifestyles [11, 12]. Albeit less frequent than in prokaryotes, horizontally transferred genes in eukaryotic genomes can clearly provide an important selective advantage for these species. The impact of HGT on all domains of life are becoming increasingly evident [13]
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