MBE Advance Access originally published online on October 11, 2006
Molecular Biology and Evolution 2007 24(1):110-121; doi:10.1093/molbev/msl138
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© 2006 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Research Articles |
Rate and Polarity of Gene Fusion and Fission in Oryza sativa and Arabidopsis thaliana
* Division of Bioengineering and Bioinformatics, Graduate School of Information Science and Technology, Hokkaido University, Kita-ku, Sapporo, Japan
Institut für Botanik III, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
Genome Research Department, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki, Japan
E-mail: yojnakam{at}ist.hokudai.ac.jp.
Accepted for publication September 25, 2006.
Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. We have identified all differentially composite or split genes in 2 fully sequenced plant genomes, Oryza sativa and Arabidopsis thaliana. Out of 10,172 orthologous gene pairs, 60 (0.6% of the total) revealed a verified fusion or fission event in either lineage after the divergence of O. sativa and A. thaliana. Polarizing these events by outgroup comparison revealed differences in the rate of gene fission but not of gene fusion in the rice and Arabidopsis lineages. Gene fission occurred at a higher rate than gene fusion in the O. sativa lineage and was furthermore more common in rice than in Arabidopsis. Nucleotide insertion bias has promoted gene fission in the O. sativa lineage, consistent with its generally longer nucleotide sequences than A. thaliana in selectively neutral regions, and with the abundance of transposable elements in rice. The divergence time of monocots and dicots (140–200 Myr) indicates that gene fusion/fission events occur at an average rate of 1 x 10–11 to 2 x 10–11 events per gene per year, 
100-fold slower than the average per site nuclear nucleotide substitution rate in these lineages. Gene fusion and fission are thus rare and slow processes in higher plant genomes; they should be of utility to address deeper evolutionary relationships among plants—and the relationship of plants to other eukaryotic lineages—where sequence-based phylogenies provide equivocal or conflicting results.
Key Words: gene fusion and fission • introns • transposable elements • plant phylogeny
Manolo Gouy, Associate Editor