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Int. J. Mol. Sci. 2016, 17(12), 1991; doi:10.3390/ijms17121991

Pseudogenes and Their Genome-Wide Prediction in Plants

1
Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
2
Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China
3
Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
4
Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
5
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
*
Author to whom correspondence should be addressed.
Academic Editor: Lam-Son Phan Tran
Received: 15 October 2016 / Revised: 20 November 2016 / Accepted: 22 November 2016 / Published: 28 November 2016
(This article belongs to the Section Molecular Botany)
View Full-Text   |   Download PDF [2205 KB, uploaded 30 November 2016]   |  

Abstract

Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu’s pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu’s pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants. View Full-Text
Keywords: pseudogenes; processed; duplicated; bioinformatics tools; plants; genome-wide pseudogenes; processed; duplicated; bioinformatics tools; plants; genome-wide
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Xiao, J.; Sekhwal, M.K.; Li, P.; Ragupathy, R.; Cloutier, S.; Wang, X.; You, F.M. Pseudogenes and Their Genome-Wide Prediction in Plants. Int. J. Mol. Sci. 2016, 17, 1991.

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