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Plant Cell Advance Online Publication
Published on January 9, 2009; 10.1105/tpc.108.063206

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Received September 10, 2008
Returned for revision December 6, 2008
Accepted December 18, 2008

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

Kousuke Hanada 1, Veronica Vallejo 2, Kan Nobuta 3, R. Keith Slotkin 4, Damon Lisch 4, Blake C. Meyers 3, Shin-Han Shiu 5, and Ning Jiang 2*

1 Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824; RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Thusumi-ku, Yokohama-shi, Kanagawa, 230-0045, Japan
2 Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
3 Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
4 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
5 Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824

* To whom correspondence should be addressed. E-mail: jiangn{at}msu.edu.

Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.




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