Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an...

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Comparing gene expression across species is crucial for evolutionary studies.
• Standard normalization methods obscure expression per gene copy or cell, potentially misrepresenting differential gene expression.
• Accurate measurement of expression per cell is needed for robust interspecies comparisons.

Purpose of the Study:

• To develop and apply an assay for estimating relative gene expression per cell.
• To compare transcriptome size with genome size in an allopolyploid relative to its progenitors.
• To infer gene dosage responses and assess dosage compensation in the allopolyploid.

Main Methods:

• Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR).
• High-throughput RNA sequencing (RNA-Seq).
• Development of an assay to estimate relative expression per cell and transcriptome size.

Main Results:

• The allopolyploid's leaf transcriptome was ~1.4-fold larger than either progenitor's transcriptome.
• Transcriptome downsizing was greater than genome downsizing in the allopolyploid.
• The majority of genes exhibited partial dosage compensation, with nonrandom distribution of homoeologue silencing.

Conclusions:

• The developed assay enables accurate comparison of expression per cell across species.
• Transcriptome size estimation is essential for interpreting gene expression data in interspecies comparisons.
• This approach provides insights into gene dosage responses and evolutionary adaptation in polyploids.