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Structural characterization and duplication modes of pseudogenes in plants
Flavia Mascagni1, Gabriele Usai1, Andrea Cavallini1
1Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
Scientific Reports
|March 6, 2021
Summary
This study characterized plant pseudogenes, revealing that dispersed pseudogenes are more common and fragmented than functional genes. Tandem and proximal duplications also generate excess pseudogenes, indicating rapid evolution in plant genomes.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Pseudogenes are non-functional DNA sequences similar to genes, arising through various duplication and mutation mechanisms.
- Understanding pseudogene formation and genomic distribution provides insights into genome evolution and plasticity.
- Comparative analysis across diverse plant species is crucial for identifying conserved and species-specific patterns.
Purpose of the Study:
- To identify and characterize pseudogene complements in five plant species, including dicots and a monocot.
- To compare the relative contribution of different duplication modes (whole genome, tandem, proximal, transposed, dispersed) to pseudogene formation versus functional gene complements.
- To investigate the genomic distribution and sequence characteristics of pseudogenes in relation to their formation mechanisms.
Main Methods:
- Utilized a bioinformatics pipeline for classifying sequence duplicates in plant genomes.
- Analyzed pseudogene and functional gene complements across Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa, Phaseolus vulgaris, and Oryza sativa.
- Compared genomic dispersion, fragmentation, sequence divergence, and flanking region conservation between pseudogenes and functional genes.
Main Results:
- Pseudogenes exhibit a greater tendency for genomic dispersion compared to functional genes.
- Dispersed pseudogenes are often fragmented with divergent flanking regions, while whole-genome duplication-derived pseudogenes show conserved flanking regions.
- Tandem and proximal duplications yield an excess of pseudogenes relative to functional genes, suggesting rapid evolution.
- Vitis vinifera displayed a notably high proportion of retro-pseudogenes.
Conclusions:
- Pseudogene formation is influenced by various duplication mechanisms, with dispersed, tandem, and proximal duplications playing significant roles.
- High rates of sequence turnover and double-strand break repair-mediated duplication contribute to pseudogene evolution.
- Comparative genomics reveals distinct evolutionary trajectories for pseudogenes versus functional genes across plant species.
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