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GENOME ANALYSIS

Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice^{1,[C],[W],[OA]}

Department of Plant Biology (C.Z., M.D.L.-S., C.R.B., S.-H.S.) and Department of Statistics and Probability (C.Z.), Michigan State University, East Lansing, Michigan 48824; J. Craig Venter Institute, Rockville, Maryland 20850 (F.T.-N.); National Center for Biotechnological Information, National Institutes of Health, Bethesda, Maryland 20894 (F.T.-N.); and Novi High School, Novi, Michigan 48375 (T.P.)

Pseudogenes () are nonfunctional genomic sequences resembling functional genes. Knowledge of s can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of s in plants. In this study, we characterized the evolution and expression patterns of s in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal s, many plant s experienced much stronger purifying selection. In addition, plant s experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became s recently. Interestingly, the regions 5' to the first stops in the s have experienced stronger selective constraints compared with 3' regions, suggesting that the 5' regions were functional for a longer period of time after the premature stops appeared. We found that few s have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, s with expressed sequence tags tend to be derived from relatively recent duplication events, indicating that expression may be due to insufficient time for complete degeneration of regulatory signals. Finally, larger protein domain families have significantly more s in general. However, while families involved in environmental stress responses have a significant excess of s, transcription factors and receptor-like kinases have lower than expected numbers of s, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant s, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.

The author 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) is: Shin-Han Shiu (shius{at}msu.edu).

^[C] Some figures in this article are displayed in color online but in black and white in the print edition.

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

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.109.140632

^* Corresponding author; e-mail shius{at}msu.edu.

Received April 29, 2009; accepted July 18, 2009; published July 29, 2009.