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Breeding by Design for Functional Rice with Genome Editing Technologies
Published on: January 3, 2025
Identification and characterization of pseudogenes in the rice gene complement
Françoise Thibaud-Nissen1, Shu Ouyang, C Robin Buell
1The J. Craig Venter Institute, 9712 Medical Center Dr, Rockville, MD 20850, USA. thibaudf@ncbi.nlm.nih.gov
BMC Genomics
|July 18, 2009
Summary
Rice pseudogenes were identified and characterized, revealing origins from gene duplication and retrotransposition. These pseudogenes, often found in fast-evolving protein families, have implications for genome annotation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The Osa1 Genome Annotation for rice (Oryza sativa L. ssp. japonica cv. Nipponbare) may misclassify pseudogenes as functional genes due to its semi-automated pipeline.
- A systematic investigation of 22,033 gene models in Osa1 Release 5 was conducted to identify potential pseudogenes based on features like lack of transcript support or altered coding regions.
Purpose of the Study:
- To identify and characterize pseudogenes within the Osa1 rice genome annotation.
- To determine the origins and prevalence of pseudogenes in rice.
Main Methods:
- Analysis of gene models for features indicative of pseudogenization, including transcript support, coding region length, untranslated region length, and paralog status in duplicated regions.
- Characterization of identified pseudogenes by similarity to functional genes and detection of frameshifts or premature stop codons.
- Determination of pseudogene origins through gene duplication and retrotransposition events.
Main Results:
- A total of 1,439 pseudogenes were identified, with significant length differences in duplicated genes being a key indicator of pseudogenization.
- Of the 816 pseudogenes with determined origins, 75% arose from gene duplication and 25% from retrotransposition.
- Pseudogenes were found in F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases, and cytochrome P450 families; 12% of pseudogenes were expressed.
Conclusions:
- Identified pseudogenes possess detectable open reading frames, distinguishing them from intergenic pseudogenes.
- Fast-evolving protein families involved in ubiquitination and secondary metabolism harbor the highest number of pseudogenes.
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