Abstract
Detecting patterns of horizontal gene transfer (HGT) in genomic sequences is an important problem, with implications for evolution, ecology, biotechnology and medicine. Extensive genetic, biochemical and genomic studies have provided a good understanding of sequence features that are associated with many (though not all) known mobile elements and mechanisms of gene transfer. This information, however, is not currently incorporated into automated methods for gene transfer detection in genomic data. In this review, we argue that automated annotation of sequence features associated with gene transfer mechanisms could be used both to build more sensitive, mechanism-specific compositional models for the detection of some types of HGT in genomic data, and to ask new questions about the classes of genes most frequently transferred by each mechanism. We then summarize the genes and sequence features associated with different mechanisms of horizontal transfer, emphasizing those that are most useful for distinguishing types of transfer when examining genomic data, and noting those classes of transfers that cannot be distinguished in genomic data using existing techniques. Finally, we describe software, databases and algorithms for identifying particular classes of mobile elements, and outline prospects for better detection of HGT based on specific mechanisms of transfer.
Highlights
The capacity of microbes to exchange genes through horizontal gene transfer (HGT) is an important phenomenon with implications for ecology, evolution, biotechnology and medicine (Ochman et al, 2000; Frost et al, 2005)
The second benefit of categorizing putative HGT genes by their mechanism of transfer is that such categorization may be used to generate a higher-confidence pool of HGT genes from a large set of putative HGT genes detected using phylogenetic or compositional methods. This can be accomplished by searching the region around each putatively transferred gene for the presence or absence of sequence features that indicate a mechanism of HGT
In order to facilitate comparisons of the types of genes transferred by different mechanisms, we review the known mechanisms of inter- and intragenomic gene transfer, emphasizing the distinct evolutionary pressures and mechanistic restraints each imposes, and the characteristics likely to prove most useful in distinguishing HGT mechanisms when examining genomic data
Summary
The capacity of microbes to exchange genes through horizontal gene transfer (HGT) is an important phenomenon with implications for ecology, evolution, biotechnology and medicine (Ochman et al, 2000; Frost et al, 2005). HGT can promote adaptation to new environments by allowing molecular innovations to be traded within ecological niches. An understanding of how microbial genomes have been shaped by HGT events has been pursued in parallel using genetic, biochemical and computational approaches. Past horizontal transfer events must be inferred from the molecular fingerprints that those events have left on extant microbial genomes. These inferences are made using computational approaches
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