Genomic island
Encyclopedia
A Genomic island is part of a genome
that has evidence of horizontal origins. The term is usually used in microbiology
, especially with regard to bacteria
. A GI can code for many functions, can be involved in symbiosis
or pathogenesis
, and may help an organism's adaptation. Many sub-classes of GIs exist that are based on the function that they confer. For example a GI associated with pathogenesis is often called a pathogenicity island
(PAIs), while GIs that contain many antibiotic resistant genes are referred to as antibiotic resistance islands. The same GI can occur in distantly related species as a result of various types of lateral gene transfer (transformation, conjugation, transduction). This can be determined by base composition analysis, as well as phylogeny estimations.
Many type 3 secretion systems
and type 4 secretion systems are located on regions of DNA called Genomic Islands.These "islands" are characterised by their large size(>10 Kb),their frequent association with tRNA-encoding genes and a different G+C content compared with the rest of the genome.Many genomic islands are flanked by repeat structures and carry fragments of other mobile elements such as phages and plasmids.Some genomic islands can excise themselves spontaneously from the chromosome and can be transferred to other suitable recipients.
Sequence based methods depend on the naturally occurring variation that exists between the genome sequence composition of different species. Genomic regions that show abnormal sequence composition (such as nucleotide bias or codon bias) suggests that these regions may have been horizontally transferred. Two major problems with these methods are that false predictions can occur due to natural variation in the genome (sometimes due to highly expressed genes) and that horizontally transferred DNA will ameliorate (change to the host genome) over time; therefore, limiting predictions to only recently acquired GIs.
Comparative genomics based methods try to identify regions that show signs that they have been horizontally transferred using information from several related species. For example, a genomic region that is present in one species, but is not present in several other related species suggests that the region may have been horizontally transferred. The alternative explanations are (i) that the region was present in the common ancestor but has been lost in all the other species being compared, or (ii) that the region was absent in the common ancestor but was acquired through mutation and selection in the species in which it is still found. The argument for multiple deletions of the region would be strengthened if there is evidence from outgroups that the region was present in the common ancestor, or if the phylogeny implies relatively few actual deletion events would be required. The argument for acquisition via mutation would be strengthened if the species with the region is known to have diverged substantially from the other species, or if the region in question is small. The plausibility of either (i) or (ii) would be modified if taxon sampling omitted many extinct species that may have possessed the region, and particularly if extinction was correlated with the presence of the region.
One example of a method that integrates several of the most accurate GI prediction methods is IslandViewer.
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
that has evidence of horizontal origins. The term is usually used in microbiology
Microbiology
Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
, especially with regard to bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
. A GI can code for many functions, can be involved in symbiosis
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
or pathogenesis
Pathogenesis
The pathogenesis of a disease is the mechanism by which the disease is caused. The term can also be used to describe the origin and development of the disease and whether it is acute, chronic or recurrent...
, and may help an organism's adaptation. Many sub-classes of GIs exist that are based on the function that they confer. For example a GI associated with pathogenesis is often called a pathogenicity island
Pathogenicity island
Pathogenicity islands are a distinct class of genomic islands acquired by microorganisms through horizontal gene transfer. They are incorporated in the genome of pathogenic organisms but are usually absent from those non-pathogenic organisms of the same or closely related species...
(PAIs), while GIs that contain many antibiotic resistant genes are referred to as antibiotic resistance islands. The same GI can occur in distantly related species as a result of various types of lateral gene transfer (transformation, conjugation, transduction). This can be determined by base composition analysis, as well as phylogeny estimations.
Many type 3 secretion systems
Type three secretion system
Type three secretion system is a protein appendage found in several Gram-negative bacteria....
and type 4 secretion systems are located on regions of DNA called Genomic Islands.These "islands" are characterised by their large size(>10 Kb),their frequent association with tRNA-encoding genes and a different G+C content compared with the rest of the genome.Many genomic islands are flanked by repeat structures and carry fragments of other mobile elements such as phages and plasmids.Some genomic islands can excise themselves spontaneously from the chromosome and can be transferred to other suitable recipients.
Computational Prediction
Various genomic island predictions programs have been developed. These tools can be broadly grouped into sequence based methods and comparative genomics/phylogeny based methods.Sequence based methods depend on the naturally occurring variation that exists between the genome sequence composition of different species. Genomic regions that show abnormal sequence composition (such as nucleotide bias or codon bias) suggests that these regions may have been horizontally transferred. Two major problems with these methods are that false predictions can occur due to natural variation in the genome (sometimes due to highly expressed genes) and that horizontally transferred DNA will ameliorate (change to the host genome) over time; therefore, limiting predictions to only recently acquired GIs.
Comparative genomics based methods try to identify regions that show signs that they have been horizontally transferred using information from several related species. For example, a genomic region that is present in one species, but is not present in several other related species suggests that the region may have been horizontally transferred. The alternative explanations are (i) that the region was present in the common ancestor but has been lost in all the other species being compared, or (ii) that the region was absent in the common ancestor but was acquired through mutation and selection in the species in which it is still found. The argument for multiple deletions of the region would be strengthened if there is evidence from outgroups that the region was present in the common ancestor, or if the phylogeny implies relatively few actual deletion events would be required. The argument for acquisition via mutation would be strengthened if the species with the region is known to have diverged substantially from the other species, or if the region in question is small. The plausibility of either (i) or (ii) would be modified if taxon sampling omitted many extinct species that may have possessed the region, and particularly if extinction was correlated with the presence of the region.
One example of a method that integrates several of the most accurate GI prediction methods is IslandViewer.