title: Pseudogenes and Their Genome-Wide Prediction in Plants.
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-annotatedArabidopsis thalianagenome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% ofA. thalianapseudogenes, 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.
authors.affiliation: Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada. xiaojin@njau.edu.cn.|Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China. xiaojin@njau.edu.cn.
authors.forename: Jin
authors.initials: J
authors.lastname: Xiao
authors.affiliation: Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada. sekhwal@gmail.com.|Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada. sekhwal@gmail.com.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Sekhwal
authors.affiliation: Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada. pingchuan.li@agr.gc.ca.
authors.forename: Pingchuan
authors.initials: P
authors.lastname: Li
authors.affiliation: Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada. rajaragupathy@gmail.com.
authors.forename: Raja
authors.initials: R
authors.lastname: Ragupathy
authors.affiliation: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada. sylvie.j.cloutier@agr.gc.ca.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Cloutier
authors.affiliation: Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China. xiuew@njau.edu.cn.
authors.forename: Xiue
authors.initials: X
authors.lastname: Wang
authors.affiliation: Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada. frank.you@agr.gc.ca.
authors.forename: Frank M
authors.initials: FM
authors.lastname: You
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020440:Gene Duplication / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics*
keywords: bioinformatics tools; duplicated; genome-wide; plants; processed; pseudogenes