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GENOME ANALYSIS

Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family^1,[w]

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (S.Z., C.C., L.M., J.S., P.G.L.); Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520–8104 (L.L., X.-W.D.); Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 (N.J.); and Department of Biology, San Francisco State University, San Francisco, California 94132 (Z.-H.H.)

The wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families in plants, plays important roles in cell expansion, pathogen resistance, and heavy-metal stress tolerance in Arabidopsis (Arabidopsis thaliana). Through a reiterative database search and manual reannotation, we identified 125 OsWAK gene family members from rice (Oryza sativa) japonica cv Nipponbare; 37 (approximately 30%) OsWAKs were corrected/reannotated from earlier automated annotations. Of the 125 OsWAKs, 67 are receptor-like kinases, 28 receptor-like cytoplasmic kinases, 13 receptor-like proteins, 12 short genes, and five pseudogenes. The two-intron gene structure of the Arabidopsis WAK/WAK-Likes is generally conserved in OsWAKs; however, extra/missed introns were observed in some OsWAKs either in extracellular regions or in protein kinase domains. In addition to the 38 OsWAKs with full-length cDNA sequences and the 11 with rice expressed sequence tag sequences, gene expression analyses, using tiling-microarray analysis of the 20 OsWAKs on chromosome 10 and reverse transcription-PCR analysis for five OsWAKs, indicate that the majority of identified OsWAKs are likely expressed in rice. Phylogenetic analyses of OsWAKs, Arabidopsis WAK/WAK-Likes, and barley (Hordeum vulgare) HvWAKs show that the OsWAK gene family expanded in the rice genome due to lineage-specific expansion of the family in monocots. Localized gene duplications appear to be the primary genetic event in OsWAK gene family expansion and the 125 OsWAKs, present on all 12 chromosomes, are mostly clustered.

The authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) are: Peggy G. Lemaux (lemauxpg{at}nature.berkeley.edu) and Shibo Zhang (shibo{at}nature.berkeley.edu).

^[w] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.069005.

^* Corresponding author; e-mail shibo{at}nature.berkeley.edu; fax 510–642–7356.

Received July 28, 2005; returned for revision August 22, 2005; accepted August 24, 2005.

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