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PMID: 15653627 Published · epublish English Evaluation Study Journal Article Research Support, Non-U.S. Gov't

Detection and characterization of horizontal transfers in prokaryotes using genomic signature.

Nucleic acids research ·Vol. 33 ·No. 1 ·2005-01-13 ·Pages e6

Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P

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.

MeSH Terms
Bacillus subtilis/genetics Computational Biology Escherichia coli/genetics Gene Transfer, Horizontal Genome, Bacterial Genomics/methods Haemophilus influenzae/genetics
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Dufraigne Christine
INSERM U 494, 91 bd de l'Hôpital 75013 Paris, France.
Fertil Bernard
Lespinats Sylvain
Giron Alain
Deschavanne Patrick
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gni004
Published
2005-01-13
Epub
2005-00-13
Pages
e6
Language
English
Region
England
NLM ID
0411011
PMCID
PMC546175
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gni004 PMC Full Text View journal details
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