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 approximately 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 approximately 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.

Figure 1

Signatures (4-letter words and 5 kb windows) along genome for Clostridium acetobutylicum, Deinococcus radiodurans and Mycobacterium tuberculosis. In this kind of displays, lines represent the frequency of words along genome, columns represent signature of windows.

Figure 2

Atypical regions for the B.subtilis genome (a) Upper panel: signatures along the genome (same as Figure 1). Lower panel: distances of local signatures to host signature (one window out of ten is shown). Distances are expressed in arbitrary units (AU). (b) Inset: close up of the 1116–1141 kb region of a putative HT, with gene composition, using 0.5 kb window and 50 bp step. Gray diamonds, host; closed diamonds, original rRNA-free regions; and multiple symbols, rRNA-containing regions.

Figure 3

Atypical regions for the H.influenzae genome. Upper panel: signatures along the genome. Lower panel: distances of local signatures to the host signature (one window out of 10 is shown). Distances are expressed in AU. Gray diamonds, host; closed diamonds, original rRNA-free regions; and multiple symbols, rRNA regions.