Pseudogenes and their genome-wide prediction in plants

J Xiao, MK Sekhwal, P Li, R Ragupathy… - International Journal of …, 2016 - mdpi.com
Pseudogenes are paralogs generated from ancestral functional genes (parents) during
genome evolution, which contain critical defects in their sequences, such as lacking a …

Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice

C Zou, MD Lehti-Shiu, F Thibaud-Nissen… - Plant …, 2009 - academic.oup.com
Pseudogenes (Ψ) are nonfunctional genomic sequences resembling functional genes.
Knowledge of Ψs can improve genome annotation and our understanding of genome …

Lowly Expressed Genes in Arabidopsis thaliana Bear the Signature of Possible Pseudogenization by Promoter Degradation

L Yang, S Takuno, ER Waters… - Molecular biology and …, 2011 - academic.oup.com
Pseudogenes are defined as nonfunctional DNA sequences with homology to functional
protein-coding genes, and they typically contain nonfunctional mutations within the …

Current trends in pseudogene detection and characterization

EC Rouchka, IE Cha - Current Bioinformatics, 2009 - ingentaconnect.com
Pseudogenes are homologous relatives of known genes that have lost their ability to
function as a transcriptional unit. Three classes of pseudogenes are known to exist …

Gene prediction and gene classes in Arabidopsis thaliana

C Mathé, P Déhais, N Pavy, S Rombauts… - Journal of …, 2000 - Elsevier
Gene prediction methods for eukaryotic genomes still are not fully satisfying. One way to
improve gene prediction accuracy, proven to be relevant for prokaryotes, is to consider more …

Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

L Wang, W Si, Y Yao, D Tian, H Araki, S Yang - PloS one, 2012 - journals.plos.org
Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic
elements derived from originally functional genes in all studied genomes within the three …

Evolutionary origins of pseudogenes and their association with regulatory sequences in plants

J Xie, Y Li, X Liu, Y Zhao, B Li, PK Ingvarsson… - The Plant …, 2019 - academic.oup.com
Pseudogenes (Ψs), nonfunctional relatives of functional genes, form by duplication or
retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis …

Origination and function of plant pseudogenes

J Xie, S Chen, W Xu, Y Zhao, D Zhang - Plant signaling & behavior, 2019 - Taylor & Francis
Pseudogenes, nonfunctional genomic sequences derived from functional protein-coding
genes, form by duplication or retrotransposition, and loss of gene function by disabling …

Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome

WA Moskal, HC Wu, BA Underwood, W Wang… - BMC genomics, 2007 - Springer
Background Several lines of evidence support the existence of novel genes and other
transcribed units which have not yet been annotated in the Arabidopsis genome. Two gene …

[PDF][PDF] Improved techniques for the identification of pseudogenes

L Coin, R Durbin - Bioinformatics, 2004 - Citeseer
Motivation: Pseudogenes are the remnants of genomic sequences of genes which are no
longer functional. They are frequent in most eukaryotic genomes, and an important resource …