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Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants
- Source :
- The Plant Cell. 31:563-578
- Publication Year :
- 2019
- Publisher :
- Oxford University Press (OUP), 2019.
-
Abstract
- Pseudogenes (Ψs), nonfunctional relatives of functional genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis provides clues to Ψ origins and effects on gene regulation. However, few systematic studies of plant Ψs have been conducted, hampering comparative analyses. Here, we examined the origin, evolution, and expression patterns of Ψs and their relationships with noncoding sequences in seven angiosperm plants. We identified ∼250,000 Ψs, most of which are more lineage specific than protein-coding genes. The distribution of Ψs on the chromosome indicates that genome recombination may contribute to Ψ elimination. Most Ψs evolve rapidly in terms of sequence and expression levels, showing tissue- or stage-specific expression patterns. We found that a surprisingly large fraction of nontransposable element regulatory noncoding RNAs (microRNAs and long noncoding RNAs) originate from transcription of Ψ proximal upstream regions. We also found that transcription factor binding sites preferentially occur in putative Ψ proximal upstream regions compared with random intergenic regions, suggesting that Ψs have conditioned genome evolution by providing transcription factor binding sites that serve as promoters and enhancers. We therefore propose that rapid rewiring of Ψ transcriptional regulatory regions is a major mechanism driving the origin of novel regulatory modules.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Genome evolution
RNA, Untranslated
Large-Scale Biology Articles
Pseudogene
Plant Science
Biology
01 natural sciences
Evolution, Molecular
Magnoliopsida
03 medical and health sciences
Regulatory Elements, Transcriptional
Enhancer
Gene
Recombination, Genetic
Genetics
Regulation of gene expression
Binding Sites
Promoter
Genomics
Cell Biology
DNA binding site
030104 developmental biology
Regulatory sequence
Mutation
DNA, Intergenic
RNA, Long Noncoding
Genome, Plant
Pseudogenes
010606 plant biology & botany
Subjects
Details
- ISSN :
- 1532298X and 10404651
- Volume :
- 31
- Database :
- OpenAIRE
- Journal :
- The Plant Cell
- Accession number :
- edsair.doi.dedup.....4d18f7673c81e8eca7ddfbe8e682f69b