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Gene expression dosage regulation in an allopolyploid fish
I Matos1, M P Machado1, M Schartl2
1CE3C-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany.
Plos One
|March 20, 2015
Summary
Allopolyploid fish (Squalius alburnoides) show significant gene expression regulation, not exact diploidization, offering evolutionary advantages. This quantitative expression flexibility aids in overcoming genomic shock and promotes survival.
Area of Science:
- Evolutionary biology
- Genomics
- Molecular biology
Background:
- Allopolyploidy, the duplication of entire genomes from different species, presents evolutionary challenges and opportunities.
- Understanding how allopolyploids, like the Iberian cyprinid Squalius alburnoides, thrive is crucial for evolutionary success.
- Previous studies suggested similar transcription levels between diploid and triploid S. alburnoides, hinting at functional diploidization.
Purpose of the Study:
- To conduct the first comparative quantitative transcriptomic analysis between diploid and triploid vertebrate allopolyploids.
- To investigate the extent of functional diploidization across the genome in S. alburnoides.
- To determine the role of gene expression regulation in the success of allopolyploids.
Main Methods:
- RNA-sequencing (RNA-seq) was performed on whole juvenile fish and adult liver tissues.
- A comparative quantitative transcriptomic analysis was conducted between diploid and triploid individuals.
- An assay to estimate relative expression per cell was used to infer transcriptome sizes.
Main Results:
- Diploid and triploid S. alburnoides exhibited similar liver transcriptome sizes.
- A significant proportion of transcripts (64% in juveniles, 44% in livers) showed less than twofold difference between diploid and triploid hybrids.
- Accurate dosage compensation was observed in 29% of juvenile transcripts and 15% of liver transcripts, indicating incomplete functional diploidization and significant gene expression downregulation in triploids.
Conclusions:
- Exact functional diploidization does not occur in triploid S. alburnoides; instead, significant gene expression downregulation is observed.
- Gene expression is not strictly proportional to gene dosage, nor is it set to a perfect diploid level in all cases.
- Quantitative expression flexibility is a key factor contributing to overcoming genomic shock and providing an evolutionary advantage to allopolyploids.
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