Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice

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