Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice      

Abstract

; and Novi High School, Novi, Michigan 48375 (T.P.) Pseudogenes (C) are nonfunctional genomic sequences resembling functional genes. Knowledge of Cs can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of Cs in plants. In this study, we characterized the evolution and expression patterns of Cs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal Cs, many plant Cs experienced much stronger purifying selection. In addition, 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. Interestingly, the regions 5# to the first stops in the Cs 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 Cs have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, Cs with expressed sequence tags tend to be derived from relatively recent duplication events, indicating that C expression may be due to insufficient time for complete degeneration of regulatory signals. Finally, larger protein domain families have significantly more Cs in general. However, while families involved in environmental stress responses have a significant excess of Cs, transcription factors and receptor-like kinases have lower than expected numbers of Cs, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant Cs, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.

Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

“…Plant pseudogenes derived from recently duplicated genes often remain transcriptionally active, presumably due to insufficient time for promoter degradation (33). We showed however that the 5Bq pseudogene participates in regulation of expression of the 5AQ and 5Dq genes at the transcript level, suggesting an active interaction between the homoeoalleles (see below).…”

Variation of Herbivore-Induced Volatile Terpenes among Arabidopsis Ecotypes Depends on Allelic Differences and Subcellular Targeting of Two Terpene Synthases, TPS02 and TPS03

“…In particular, stress-responsive gene families such as the TPS family have elevated levels of pseudogenization, which can be interpreted as a rapid turnover of genes under varying selection pressures Zou et al, 2009). Analysis of the TPS02-TPS03 gene pair in Col-0 and Ws demonstrated that either one of the duplicated genes can lose function.…”

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

“…Combining the pseudogene data from intergenic regions (genomic regions between annotated genes) and annotated genes (Benovoy and Drouin, 2006;Thibaud-Nissen et al, 2009;Zou et al, 2009), the percentage of pseudogenes in Arabidopsis thaliana and O. sativa ssp japonica was 16 and 42%, respectively. We observed similar rates of 28% in the two soybean homoeologs and 29% for Phaseolus, intermediate to Arabidopsis and rice.…”

“…We found that the percentage of pseudogenes with paralogs to all pseudogenes was 56 and 61% for Gm8 and Gm15, respectively. In rice, two studies focusing on either intergenic regions (Zou et al, 2009) or on annotated genes only found that the percentage of pseudogenes with paralogs was 28 and 75%, respectively. In Arabidopsis, the percentage of pseudogenes with paralogs was 47% (Zou et al, 2009).…”

“…In rice, two studies focusing on either intergenic regions (Zou et al, 2009) or on annotated genes only found that the percentage of pseudogenes with paralogs was 28 and 75%, respectively. In Arabidopsis, the percentage of pseudogenes with paralogs was 47% (Zou et al, 2009). Therefore, our results from these two soybean homoeologous regions are concordant with previous studies.…”