Abstract
A genome-wide computational analysis of overlapping genes in various prokaryotic genomes was conducted to study the evolutionary rates of the formation and degradation of overlapping genes. Overlapping genes are adjacent genes that overlap partially or entirely. Overlapping gene pairs extracted from complete bacterial genome sequences were classified into three directional patterns, namely, 'convergent' (→←), 'unidirectional' (→→), and 'divergent' (←→). Divergent overlapping genes were rare compared to the other two patterns. We also compared the structures of overlapping genes that are not conserved in the homologous genes of different species. We found that overlapping genes are mainly generated from gene pairs with short intergenic regions. Overlapping genes caused by mutations at the 3′-end of genes occur more frequently than overlapping genes generated by mutations at the 5′-end of genes in closely related species. In contrast, gene overlaps due to mutations at the 5′-ends accumulate in distant species. These differences presumably correlate to the genomic divergence among species. The evolution of these overlapping gene structures is probably related to the evolutionary time scale, which suggests that the evolution of overlapping genes occurs at a universal mutation rate across species.
| Original language | English |
|---|---|
| Pages (from-to) | 181-187 |
| Number of pages | 7 |
| Journal | Gene |
| Volume | 323 |
| Issue number | 1-2 |
| DOIs | |
| Publication status | Published - 2003 Dec 24 |
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Keywords
- Bacterial genome
- Comparative genomics
- Intergenic region
- Mutation rate
ASJC Scopus subject areas
- Genetics
Cite this
On dynamics of overlapping genes in bacterial genomes. / Fukuda, Yoko; Nakayama, Yoichi; Tomita, Masaru.
In: Gene, Vol. 323, No. 1-2, 24.12.2003, p. 181-187.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - On dynamics of overlapping genes in bacterial genomes
AU - Fukuda, Yoko
AU - Nakayama, Yoichi
AU - Tomita, Masaru
PY - 2003/12/24
Y1 - 2003/12/24
N2 - A genome-wide computational analysis of overlapping genes in various prokaryotic genomes was conducted to study the evolutionary rates of the formation and degradation of overlapping genes. Overlapping genes are adjacent genes that overlap partially or entirely. Overlapping gene pairs extracted from complete bacterial genome sequences were classified into three directional patterns, namely, 'convergent' (→←), 'unidirectional' (→→), and 'divergent' (←→). Divergent overlapping genes were rare compared to the other two patterns. We also compared the structures of overlapping genes that are not conserved in the homologous genes of different species. We found that overlapping genes are mainly generated from gene pairs with short intergenic regions. Overlapping genes caused by mutations at the 3′-end of genes occur more frequently than overlapping genes generated by mutations at the 5′-end of genes in closely related species. In contrast, gene overlaps due to mutations at the 5′-ends accumulate in distant species. These differences presumably correlate to the genomic divergence among species. The evolution of these overlapping gene structures is probably related to the evolutionary time scale, which suggests that the evolution of overlapping genes occurs at a universal mutation rate across species.
AB - A genome-wide computational analysis of overlapping genes in various prokaryotic genomes was conducted to study the evolutionary rates of the formation and degradation of overlapping genes. Overlapping genes are adjacent genes that overlap partially or entirely. Overlapping gene pairs extracted from complete bacterial genome sequences were classified into three directional patterns, namely, 'convergent' (→←), 'unidirectional' (→→), and 'divergent' (←→). Divergent overlapping genes were rare compared to the other two patterns. We also compared the structures of overlapping genes that are not conserved in the homologous genes of different species. We found that overlapping genes are mainly generated from gene pairs with short intergenic regions. Overlapping genes caused by mutations at the 3′-end of genes occur more frequently than overlapping genes generated by mutations at the 5′-end of genes in closely related species. In contrast, gene overlaps due to mutations at the 5′-ends accumulate in distant species. These differences presumably correlate to the genomic divergence among species. The evolution of these overlapping gene structures is probably related to the evolutionary time scale, which suggests that the evolution of overlapping genes occurs at a universal mutation rate across species.
KW - Bacterial genome
KW - Comparative genomics
KW - Intergenic region
KW - Mutation rate
UR - http://www.scopus.com/inward/record.url?scp=0345490693&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0345490693&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2003.09.021
DO - 10.1016/j.gene.2003.09.021
M3 - Article
C2 - 14659892
AN - SCOPUS:0345490693
VL - 323
SP - 181
EP - 187
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1-2
ER -