Abstract
Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.
| Original language | English |
|---|---|
| Pages (from-to) | 267-276 |
| Number of pages | 10 |
| Journal | DNA Research |
| Volume | 15 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - 2008 Dec 1 |
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Keywords
- Amelioration
- Dinucleotide frequency
- Essential genes
- Horizontal transfer
- Molecular evolution
ASJC Scopus subject areas
- Genetics
- Molecular Biology
- Medicine(all)
Cite this
Detecting horizontally transferred and essential genes based on dinucleotide relative abundance. / Baran, Robert H.; Ko, Hanseok.
In: DNA Research, Vol. 15, No. 5, 01.12.2008, p. 267-276.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Detecting horizontally transferred and essential genes based on dinucleotide relative abundance
AU - Baran, Robert H.
AU - Ko, Hanseok
PY - 2008/12/1
Y1 - 2008/12/1
N2 - Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.
AB - Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.
KW - Amelioration
KW - Dinucleotide frequency
KW - Essential genes
KW - Horizontal transfer
KW - Molecular evolution
UR - http://www.scopus.com/inward/record.url?scp=56049115597&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=56049115597&partnerID=8YFLogxK
U2 - 10.1093/dnares/dsn021
DO - 10.1093/dnares/dsn021
M3 - Article
C2 - 18799480
AN - SCOPUS:56049115597
VL - 15
SP - 267
EP - 276
JO - DNA Research
JF - DNA Research
SN - 1340-2838
IS - 5
ER -