Detection and characterization of horizontal transfers in prokaryotes using genomic signature - PubMed (original) (raw)
Detection and characterization of horizontal transfers in prokaryotes using genomic signature
Christine Dufraigne et al. Nucleic Acids Res. 2005.
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.
Figures
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.
Similar articles
- Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus.
Mallet LV, Becq J, Deschavanne P. Mallet LV, et al. BMC Genomics. 2010 Mar 12;11:171. doi: 10.1186/1471-2164-11-171. BMC Genomics. 2010. PMID: 20226043 Free PMC article. - (Patho-)Genomics of Escherichia coli.
Dobrindt U. Dobrindt U. Int J Med Microbiol. 2005 Oct;295(6-7):357-71. doi: 10.1016/j.ijmm.2005.07.009. Int J Med Microbiol. 2005. PMID: 16238013 Review. - Detection and analysis of horizontal gene transfer in herpesvirus.
Fu M, Deng R, Wang J, Wang X. Fu M, et al. Virus Res. 2008 Jan;131(1):65-76. doi: 10.1016/j.virusres.2007.08.009. Epub 2007 Oct 1. Virus Res. 2008. PMID: 17905462 - Designed horizontal transfer of stable giant DNA released from Escherichia coli.
Kaneko S, Itaya M. Kaneko S, et al. J Biochem. 2010 Jun;147(6):819-22. doi: 10.1093/jb/mvq012. Epub 2010 Feb 9. J Biochem. 2010. PMID: 20145021 - Computational comparisons of model genomes.
Ouzounis C, Casari G, Sander C, Tamames J, Valencia A. Ouzounis C, et al. Trends Biotechnol. 1996 Aug;14(8):280-5. doi: 10.1016/0167-7799(96)10043-3. Trends Biotechnol. 1996. PMID: 8987458 Review.
Cited by
- The Theory of Gene Family Histories.
Hellmuth M, Stadler PF. Hellmuth M, et al. Methods Mol Biol. 2024;2802:1-32. doi: 10.1007/978-1-0716-3838-5_1. Methods Mol Biol. 2024. PMID: 38819554 - Compositional Structure of the Genome: A Review.
Bernaola-Galván P, Carpena P, Gómez-Martín C, Oliver JL. Bernaola-Galván P, et al. Biology (Basel). 2023 Jun 13;12(6):849. doi: 10.3390/biology12060849. Biology (Basel). 2023. PMID: 37372134 Free PMC article. Review. - Genomic Signature in Evolutionary Biology: A Review.
de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. de la Fuente R, et al. Biology (Basel). 2023 Feb 16;12(2):322. doi: 10.3390/biology12020322. Biology (Basel). 2023. PMID: 36829597 Free PMC article. Review. - INSIDER: alignment-free detection of foreign DNA sequences.
Tay AP, Hosking B, Hosking C, Bauer DC, Wilson LOW. Tay AP, et al. Comput Struct Biotechnol J. 2021 Jun 29;19:3810-3816. doi: 10.1016/j.csbj.2021.06.045. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 34285780 Free PMC article. - The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis.
Noroy C, Meyer DF. Noroy C, et al. PLoS Comput Biol. 2021 Jul 12;17(7):e1008788. doi: 10.1371/journal.pcbi.1008788. eCollection 2021 Jul. PLoS Comput Biol. 2021. PMID: 34252087 Free PMC article.
References
- Eisen J.A. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 2000;10:606–611. - PubMed
- Jeltsch A., Pingoud A. Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems. J. Mol. Evol. 1996;42:91–96. - PubMed
- Lan R., Reeves P.R. Gene transfer is a major factor in bacterial evolution. Mol. Biol. Evol. 1996;13:47–55. - PubMed
- Smith M.W., Feng D.F., Doolittle R.F. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 1992;17:489–493. - PubMed
- Dutta C., Pan A. Horizontal gene transfer and bacterial diversity. J. Biosci. 2002;27:27–33. - PubMed
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources