Detection and characterization of horizontal transfers in prokaryotes using genomic signature

Abstract

Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-specific even in DNA fragments as short as 1 kb. The genomic signature is therefore proposed as a tool to detect HTs. Since DNA transfers originate from species with a signature different from those of the recipient species, the analysis of local variations of signature along recipient genome may allow for detecting exogenous DNA. The strategy consists in (i) scanning the genome with a sliding window, and calculating the corresponding local signature (ii) evaluating its deviation from the signature of the whole genome and (iii) looking for similar signatures in a database of genomic signatures. A total of 22 prokaryote genomes are analyzed in this way. It has been observed that atypical regions make up ∼6% of each genome on the average. Most of the claimed HTs as well as new ones are detected. The origin of putative DNA transfers is looked for among ∼12 000 species. Donor species are proposed and sometimes strongly suggested, considering similarity of signatures. Among the species studied, Bacillus subtilis, Haemophilus Influenzae and Escherichia coli are investigated by many authors and give the opportunity to perform a thorough comparison of most of the bioinformatics methods used to detect HTs.

The Purity Measure for Genomic Regions Leads to Horizontally Transferred Genes

“…14 This composition-based approach is also widely used for characterization of horizontally transferred genes. [17][18][19][20] Basically, in those methods, only the compositions of low-order nucleotide, i.e. mono-, di-and tri-nucleotide, are considered.…”

Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Noncoalescent Genes

“…Indeed, focusing on genomic regions with anomalous GC content is a common method for identifying genes that have undergone HGT. More complex consequences of base composition and mutation patterns, such as the frequencies of DNA oligonucleotides ('words') in coding or noncoding regions, have also been used to flag potential HGT genes, particularly in bacteria (Medrano-Sato et al 2004;Dufraigne et al 2005). Like the test above, the results of GC or DNA word frequency analysis should be considered suggestive, but not conclusive.…”

Risks from GMOs due to Horizontal Gene Transfer

“…Thus, if codon usage, GC content or oligonucleotide signatures differ significantly from the mean for a given genome, then HGT may be invoked (Dufraigne et al, 2005;Hooper and Berg, 2002;Kanaya et al, 2001;Karlin et al, 1998;Lawrence and Ochman, 1998;Sandberg et al, 2001;Tsirigos and Rigoutsos, 2005). A significant fraction of many prokaryote genomes, up to 20%, has been classified as recent HGTs according to these criteria (Garcia-Vallve et al, 2003).…”