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Age and detection of retroprocessed pseudogenes in murine rodents
Felix Friedberg1, Allen R Rhoads
1Department of Biochemistry and Molecular Biology, Howard University, College of Medicine, Washington, DC 20059, USA. ffriedberg@howard.edu
Abstract:
Retroprocessed pseudogenes, calmodulin II (psi1, psi2, and psi3 CALMII), psi alpha-tubulin, pi-glutathione S-transferase (psi pi-GST) from rat, lactic acid dehydrogenase (psi LDH) from mouse, and heat shock protein 60 chaperonin (psi HSP60) from Chinese hamster, were examined for their presence in these species by polymerase chain reaction (PCR). Pseudogenes of these murine rodents were detected by PCR only in those species in which the genes were originally identified, suggesting that the selected pseudogene of one species arose too recently to be detected in the genomes of the other rodent species. The calculated ages of the rodent pseudogenes ranged from 1.7 Myr (psi alpha-tubulin) to 7.5 Myr (psi3 CALMII) when employing a homologous functional gene of the taxon as a reference in the relative rate test with the mouse or rat as the outgroup. Given the high rate of divergence of the genes of rodents relative to other species, selection of an outgroup with similar mutation rates seems warranted. To justify further the conclusion that the selected pseudogenes were indeed retroprocessed after these three taxa diverged, the presence of the pseudogenes in the genome of different rat species was examined. The existence of psi3 CALMII and psi alpha-tubulin pseudogenes of Rattus norvegicus among species belonging to Rattus sensu stricto is evidence for the common ancestry of this group.
Insights
Retroprocessed pseudogenes were detected in rodent species using PCR, suggesting recent evolutionary origins. The ages of these pseudogenes, like calmodulin II (CALMII) and alpha-tubulin, were estimated, providing insights into rodent genome evolution.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Retroprocessed pseudogenes are non-functional gene copies formed by reverse transcription of mRNA and integration into the genome.
- Understanding pseudogene evolution provides insights into genome dynamics and functional gene regulation.
Purpose of the Study:
- To investigate the presence and evolutionary age of specific retroprocessed pseudogenes in rodent species.
- To determine if pseudogene distribution reflects species-specific gene duplication events or broader evolutionary patterns.
Main Methods:
- Polymerase chain reaction (PCR) was used to detect the presence of pseudogenes (e.g., CALMII, alpha-tubulin, pi-GST, LDH, HSP60) in different rodent species.
- Relative rate tests, utilizing homologous functional genes and specific outgroups (mouse or rat), were employed to estimate pseudogene divergence times.
Main Results:
- Detected pseudogenes were largely confined to the species where their parent genes were originally identified, indicating recent retropositional events.
- Estimated ages of rodent pseudogenes ranged from 1.7 million years (psi alpha-tubulin) to 7.5 million years (psi3 CALMII).
- The presence of specific pseudogenes (psi3 CALMII, psi alpha-tubulin) in multiple Rattus species supports their common ancestry.
Conclusions:
- The distribution and estimated ages of these pseudogenes suggest they arose relatively recently after the divergence of the studied rodent taxa.
- The findings highlight the utility of pseudogenes as molecular clocks for studying recent evolutionary events in rodents.
- Pseudogene analysis in Rattus species provides evidence for their evolutionary relationships.