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First published online April 22, 2004; 10.1105/tpc.020834

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The Plant Cell 16:1220-1234 (2004)
© 2004 American Society of Plant Biologists

Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice

Shin-Han Shiua, Wojciech M. Karlowskib, Runsun Pana,d, Yun-Huei Tzenga,c, Klaus F. X. Mayerb and Wen-Hsiung Lia,1

a Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
b Munich Information Center for Protein Sequences/Institute of Bioinformatics, GSF, National Research Center for Environment and Health, Neuherberg 85764, Germany
c Department of Mathematics, National Tsing Hua University, Hsinchu, Taiwan 300
d Institute of Information Science, Academia Sinica, Taiwan 115

1 To whom correspondence should be addressed. E-mail whli{at}uchicago.edu; fax 773-702-9740.

Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that large-scale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis–rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.




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