期刊
G3-GENES GENOMES GENETICS
卷 4, 期 1, 页码 19-27出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.113.005652
关键词
overlapping genes; unidirectional genes; prokaryotic genomes; overlap length distribution
资金
- European Social Fund
- Operational Human of Potential Program (POPH)
- Portuguese Institution Fundacao para a Ciencia e a Tecnologia [SFRH/BPD/70654/2010]
- European Research Council [ERC-2007-Stg 203161-PHYGENOM]
Prokaryotic unidirectional overlapping genes can be originated by disrupting and replacing of the start or stop codon of one protein-coding gene with another start or stop codon within the adjacent gene. However, the probability of disruption and replacement of a start or stop codon may differ significantly depending on the number and redundancy of the start and stop codons sets. Here, we performed a simulation study of the formation of unidirectional overlapping genes using a simple model of nucleotide change and contrasted it with empirical data. Our results suggest that overlaps originated by an elongation of the 3 '-end of the upstream gene are significantly more frequent than those originated by an elongation of the 5 '-end of the downstream gene. According to this, we propose a model for the creation of unidirectional overlaps that is based on the disruption probabilities of start codon and stop codon sets and on the different probabilities of phase 1 and phase 2 overlaps. Additionally, our results suggest that phase 2 overlaps are formed at higher rates than phase 1 overlaps, given the same evolutionary time. Finally, we propose that there is no need to invoke selection to explain the prevalence of long phase 1 unidirectional overlaps. Rather, the overrepresentation of long phase 1 relative to long phase 2 overlaps might occur because it is highly probable that phase 2 overlaps are retained as short overlaps by chance. Such a pattern is stronger if selection against very long overlaps is included in the model. Our model as a whole is able to explain to a large extent the empirical length distribution of unidirectional overlaps in prokaryotic genomes.
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