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Genomic Islands (genomic + island)

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Life Sciences100%

Selected Abstracts

Genomic islands of speciation or genomic islands and speciation?

MOLECULAR ECOLOGY, Issue 5 2010
THOMAS L. TURNER
Populations of the malaria mosquito, Anopheles gambiae, are comprised of at least two reproductively isolated, sympatric populations. In this issue, White et al. (2010) use extensive sampling, high-density tiling microarrays, and an updated reference genome to clarify and expand our knowledge of genomic differentiation between these populations. It is now clear that DNA near the centromeres of all three chromosomes are in near-perfect disequilibrium with each other. This is in stark contrast to the remaining 97% of the assembled genome, where fixed differences between populations have not been found, and many polymorphisms are shared. This pattern, coupled with direct evidence of hybridization in nature, supports models of "mosaic" speciation, where ongoing hybridization homogenizes variation in most of the genome while loci under strong selection remain in disequilibrium with each other. However, unambiguously demonstrating that selection maintains the association of these pericentric "speciation islands" in the face of gene flow is difficult. Low recombination at all three loci complicates the issue, and increases the probability that selection unrelated to the speciation process alters patterns of variation in these loci. Here, we discuss these different scenarios in light of this new data. [source]

Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia

ENVIRONMENTAL MICROBIOLOGY, Issue 3 2003
Tina Andrea Müller
Summary The genetic structure of two Ralstonia spp., strain JS705 and strain JS745, isolated from the same groundwater aquifer, was characterized with respect to the degradation capacities for toluene and chlorobenzene degradation. Cosmid library construction, cloning, DNA sequencing and mating experiments indicated that the genes for chlorobenzene degradation in strain JS705 were a mosaic of the clc genes, previously described for Pseudomonas sp. strain B13, and a 5 kb fragment identical to strain JS745. The 5 kb fragment identical to both JS705 and JS745 was flanked in JS705 by one complete and one incomplete insertion (IS) element. This suggested involvement of the IS element in mobilizing the genes from JS745 to JS705, although insertional activity of the IS element in its present configuration could not be demonstrated. The complete genetic structure for chlorobenzene degradation in strain JS705 resided on a genomic island very similar to the clc element (Ravatn, R., Studer, S., Springael, D., Zehnder, A.J., van der Meer, J.R. 1998. Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. J Bacteriol 180: 4360,4369). The unique reconstruction of formation of a metabolic pathway through the activity of IS elements and a genomic island in the chlorobenzene-degrading strain JS705 demonstrated how pathway evolution can occur under natural conditions in a few ,steps'. [source]

Approaches to prokaryotic biodiversity: a population genetics perspective

ENVIRONMENTAL MICROBIOLOGY, Issue 11 2002
Francisco Rodríguez-Valera
Summary The study of prokaryotic diversity has blossomed during the last 10,15 years as a result of the introduction of molecular identification, mostly based on direct 16S rRNA gene polymerase chain reaction (PCR) amplification and sequencing from natural samples. A large amount of information exists about the diversity of this specific gene. However, data from the field of bacterial population genetics and genomics make questionable the value of information regarding just one gene. Even if we accept 16S rRNA genes as useful for species identification, intraspecific variation in bacteria is so high that species catalogues are often of little value. The gene pools represented by an operational species are yet impossible to predict. On the other hand, adaptive features in prokaryotes are often coded in gene clusters (genomic islands) that can be cloned directly from the environment, sequenced and even expressed in a surrogate host. Thus, the study of the environmental genome or metagenome appears as an alternative that could eventually lead to a more realistic understanding of prokaryotic biodiversity, provide biotechnology with new tools and maybe even contribute to develop a model of prokaryotic evolution. [source]

Genomic islands of speciation or genomic islands and speciation?

MOLECULAR ECOLOGY, Issue 5 2010
THOMAS L. TURNER
Populations of the malaria mosquito, Anopheles gambiae, are comprised of at least two reproductively isolated, sympatric populations. In this issue, White et al. (2010) use extensive sampling, high-density tiling microarrays, and an updated reference genome to clarify and expand our knowledge of genomic differentiation between these populations. It is now clear that DNA near the centromeres of all three chromosomes are in near-perfect disequilibrium with each other. This is in stark contrast to the remaining 97% of the assembled genome, where fixed differences between populations have not been found, and many polymorphisms are shared. This pattern, coupled with direct evidence of hybridization in nature, supports models of "mosaic" speciation, where ongoing hybridization homogenizes variation in most of the genome while loci under strong selection remain in disequilibrium with each other. However, unambiguously demonstrating that selection maintains the association of these pericentric "speciation islands" in the face of gene flow is difficult. Low recombination at all three loci complicates the issue, and increases the probability that selection unrelated to the speciation process alters patterns of variation in these loci. Here, we discuss these different scenarios in light of this new data. [source]

Conjugative transposons: the tip of the iceberg

MOLECULAR MICROBIOLOGY, Issue 3 2002
Vincent Burrus
Summary Elements that excise and integrate, such as prophages, and transfer by conjugation, such as plasmids, have been found in various bacteria. These elements appear to have a diversified set of characteristics including cell-to-cell contact using pili or cell aggregation, transfer of single-stranded or double-stranded DNA, low or high specificity of integration and serine or tyrosine recombinases. This has led to a highly heterogeneous nomenclature, including conjugative transposons, integrative ,plasmids', genomic islands and numerous unclassified elements. However, all these elements excise by site-specific recombination, transfer the resulting circular form by conjugation and integrate by recombination between a specific site of this circular form and a site in the genome of their host. Whereas replication of the circular form probably occurs during conjugation, this replication is not involved in the maintenance of the element. In this review, we show that these elements share very similar characteristics and, therefore, we propose to classify them as integrative and conjugative elements (ICEs). These elements evolve by acquisition or exchanges of modules with various transferable elements including at least ICEs and plasmids. The ICEs are probably widespread among the bacteria. [source]

Pathogenicity islands: a molecular toolbox for bacterial virulence

CELLULAR MICROBIOLOGY, Issue 11 2006
Ohad Gal-Mor
Summary Pathogenicity islands (PAIs) are distinct genetic elements on the chromosomes of a large number of bacterial pathogens. PAIs encode various virulence factors and are normally absent from non-pathogenic strains of the same or closely related species. PAIs are considered to be a subclass of genomic islands that are acquired by horizontal gene transfer via transduction, conjugation and transformation, and provide ,quantum leaps' in microbial evolution. Data based on numerous sequenced bacterial genomes demonstrate that PAIs are present in a wide range of both Gram-positive and Gram-negative bacterial pathogens of humans, animals and plants. Recent research focused on PAIs has not only led to the identification of many novel virulence factors used by these species during infection of their respective hosts, but also dramatically changed our way of thinking about the evolution of bacterial virulence. [source]

Distinctiveness in the face of gene flow: hybridization between specialist and generalist gartersnakes

MOLECULAR ECOLOGY, Issue 18 2008
BENJAMIN M. FITZPATRICK
Abstract Patterns of divergence and polymorphism across hybrid zones can provide important clues as to their origin and maintenance. Unimodal hybrid zones or hybrid swarms are composed predominantly of recombinant individuals whose genomes are patchworks of alleles derived from each parental lineage. In contrast, bimodal hybrid zones contain few identifiable hybrids; most individuals fall within distinct genetic clusters. Distinguishing between hybrid swarms and bimodal hybrid zones can be important for taxonomic and conservation decisions regarding the status and value of hybrid populations. In addition, the causes of bimodality are important in understanding the generation and maintenance of biological diversity. For example, are distinct clusters mostly reproductively isolated and co-adapted gene complexes, or can distinctiveness be maintained by a few ,genomic islands' despite rampant gene flow across much of the genome? Here we focus on three patterns of distinctiveness in the face of gene flow between gartersnake taxa in the Great Lakes region of North America. Bimodality, the persistence of distinct clusters of genotypes, requires strong barriers to gene flow and supports recognition of distinct specialist (Thamnophis butleri) and generalist (Thamnophis radix) taxa. Concordance of DNA-based clusters with morphometrics supports the hypothesis that trophic morphology is a key component of divergence. Finally, disparity in the level of differentiation across molecular markers (amplified fragment length polymorphisms) indicates that distinctiveness is maintained by strong selection on a few traits despite high gene flow currently or in the recent past. [source]