Mycoplasma genitalium Mycoplasma
pneumoniae

Evolution of Overlapping Genes: Comparative Genomics
ofandYoko Fukuda 12

t95775yf@sfc.keio.ac.jp
123Takanori Washio 13

washy@sfc.keio.ac.jp

Masaru Tomita 12
mt@sfc.keio.ac.jp

Laboratory for Bioinformatics
Department of Environmental Information
Graduate School of Media and Governance
Keio University, 5322 Endo, Fujisawa, 252-8520 Japan

1 Introduction
Many overlapping genes have been identi ed in the genomes of procaryotes, bacteriophages, animalviruses, and mitochondria, some of which have been reported to have functional roles [1], but theirevolutionary origin is not clearly understood. We systematically analyzed all overlapping genes in thegenomes of two closely related species, Mycoplasma genitalium [2] and Mycoplasma pneumoniae [3].
In particular, careful comparisons were made for the homologous genes that are overlapped in one
species but not in the other.

2 Materials and Methods
We rst list all overlapping genes in their genomes according to the annotations in the databases [2, 3].
For each overlapping gene pair in one species, we aligned the sequence, using ClustalW [4], with thesequence of the homologous part of the other species. We then classi ed all the cases according to
the three directional patterns as described in Fig. 1: \end-on", \uni-directional", and \head-on". For
those genes that overlap in one species but not in the other, we made careful analyses in order to infer
the cause of the overlapping. The putative causes of these events of overlapping were then classi ed
into several types.

3 Results and Discussion
In the genome of M. genitalium, there are 155 overlapping gene pairs, according to the TIGR annotation. The genome of M. pneumoniae, on the other hand, contains 160 overlapping gene pairs. Many
parts of genome sequences of these two species are homologous. There are 134 homologous overlapping
gene pairs which exist in both species.
The other 21 and 26 overlapping gene pairs are found only in M. genitalium and M. pneumoniae,respectively. Comparative analysis of these gene sequences allows us to propose a model of how
overlapping genes emerged in the course of evolution.
It was found that overlapping genes were generated primarily due to the loss of a stop codon ineither gene, the absence of which resulted in elongation of the 3' end of the gene's coding region.
More speci cally, the loss of the stop codon took place as a result of the following events: deletion of
the stop codon (72.1 %); point mutation at the stop codon (4.7%); and frame shift at the end of thecoding region (7.0%). Overlapping genes, in a sense, might be thought of as the results of evolutionarypressure to minimize genome size. However, our analysis indicates that many overlapping genes, at254

"end-on overlapping"gene Agene B"uni-directional overlapping"gene Agene B"head-on overlapping"gene Agene B

Figure 1: Three patterns of overlapping genes.
Table 1: summary of inferred causes of gene overlapping.

!

end-on ()uni-directional (total!!

deletion point mutation frame shift unknown
812024117)
32

2

37

least in the genomes of M. genitalium and M. pneumoniae, are merely due to incidental elongation of
the coding regions.

Acknowledgements
This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas `Genome
Science' from The Ministry of Education, Science, Sports and Culture in Japan.

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[2] Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R.D., Bult,C.J., Kerlavage, A.R., Sutton, G., Kelley, J.M., et al.,The minimal gene complement of Mycoplasma genitalium, Science, 270:397{403, 1995.
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[4] Higgins, D.G., Bleasby, A.J. and Fuchs, R., CLUSTAL V: improved software for multiple sequencealignment. Computer Applications in the Biosciences (CABIOS), 8(2):189{191, 1992.
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