Abstract
Pseudogenes (Psi) are nonfunctional genomic sequences resembling functional genes. Knowledge of Psis can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of Psis in plants. In this study, we characterized the evolution and expression patterns of Psis in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal Psis, many plant Psis experienced much stronger purifying selection. In addition, plant Psis experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became Psis recently. Interestingly, the regions 5' to the first stops in the Psis 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 Psis have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, Psis 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 Psis in general. However, while families involved in environmental stress responses have a significant excess of Psis, transcription factors and receptor-like kinases have lower than expected numbers of Psis, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant Psis, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.
Highlights
Pseudogenes (C) are nonfunctional genomic sequences resembling functional genes
Because Cs are similar to functional genes, a large number of Cs are misidentified as potentially functional genes during the genome annotation process (Arabidopsis Genome Initiative, 2000; Lander et al, 2001; Mounsey et al, 2002; Mouse Genome Sequencing Consortium, 2002)
We determined the number of annotated genes that are presumably functional and the number of Cs that have evidence of expression based on (1) putative unique transcript (PUT), (2) massively parallel signature sequencing (MPSS) tags, and (3) tiling array data
Summary
Pseudogenes (C) are nonfunctional genomic sequences resembling functional genes. Knowledge of Cs can improve genome annotation and our understanding of genome evolution. Plant Cs experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became Cs recently. The most prominent example is a nitric oxide synthase (NOS) C that contains an approximately 140-bp region that forms a heteroduplex with the functional NOS transcript and suppresses the translation of NOS protein (Korneev et al, 1999) Another example of C function at the RNA level is the Makorin1-p1 C, which potentially regulates the stability of its homologous coding gene transcript (Hirotsune et al, 2003) and experiences nonneutral evolution (Podlaha and Zhang, 2004); its function remains controversial (Gray et al, 2006). Cs have been extensively studied in various animal genomes and yeast (Torrents et al, 2003; Zhang et al, 2003, 2004; Lafontaine et al, 2004; Zheng et al, 2007)
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