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Published on December 31, 2008; 10.1104/pp.108.131656

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Received October 26, 2008
Accepted December 21, 2008

Highly diversified molecular evolution of downstream transcription start sites in Oryza sativa and Arabidopsis thaliana

Tsuyoshi Tanaka , Kanako O. Koyanagi , and Takeshi Itoh *

Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences Tsukuba, Ibaraki 305-8602, Japan; Graduate School of Information Science and Technology, Hokkaido University Sapporo, Hokkaido 060-0814, Japan

* Corresponding author; email: taitoh{at}affrc.go.jp.

Alternative usage of transcription start sites (TSSs) is one of the key mechanisms to generate gene variation in eukaryotes. Here we show diversified molecular evolution of TSSs in remotely-related flowering plants, Oryza sativa and Arabidopsis thaliana, by comprehensive analyses of large collections of full-length cDNAs and genome sequences. We determined 45,917 representative TSSs within 23,445 loci of O. sativa and 35,313 TSSs within 16,964 loci of A. thaliana; about two TSSs per locus in either species. The nucleotide features around TSSs displayed distinct patterns when the most upstream TSSs were compared to downstream TSSs. We found that GC- and AT-skew was clearly different between upstream and downstream TSSs, and that this difference was commonly observed in O. sativa and A. thaliana. Relative entropy analysis revealed that the most upstream TSSs had retained canonical cis-elements, whereas downstream TSSs showed atypical nucleotide features. Expression patterns were distinguishable between upstream and downstream TSSs. These results indicate that plant TSSs were generally diversified in downstream regions, resulting in the development of new gene expression patterns. Furthermore, our comparative analysis of TSS variation between the species showed a positive correlation between TSS number and gene conservation. O. sativa and A. thaliana might have evolved novel TSSs in an independent manner, which led to diversification of these two species.






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