Coate, Jeremy E. , Doyle, Jeff J. .
How large is a polyploid’s transcriptome, and why should we care?
An allotetraploid combines the genomes of its progenitors, and thus has roughly twice as many genes as a diploid. But what about its transcriptome? An individual gene in a polyploid may show any of several expression patterns relative to its diploid progenitors, of which the most obvious alternatives are a 1:1 dosage effect (summing the expression levels of the two parents), or expression at a diploid level (dosage compensation or midparent expression, depending on the diploid expression patterns). Intermediate and transgressive effects are also possible. The overall size of the allopolyploid transcriptome is the sum of these individual responses. Microarray and next-generation sequencing methods normalize to the transcriptome, and thus do not permit estimation of relative transcriptome sizes, which is necessary to interpret expression profiling data across species and ploidy levels. We describe a quantitative RT-PCR (qRT-PCR) assay that facilitates estimates of expression per cell. When used in conjunction with transcript profiling data, this estimate makes it possible to compare the sizes of whole transcriptomes, which in turn allows gene expression levels to be compared across species. We applied this approach, using high throughput RNA sequencing (RNA-Seq), to a recently formed allotetraploid (Glycine dolichocarpa; Leguminosae: Phaseoleae), and showed that its leaf transcriptome was approximately 1.4-fold larger than either progenitor transcriptome. This departure from additive expression was not simply a function of gene loss: of over 10,000 genes with sufficient RNA-seq data, 87% possessed both homoeologues contributed from their diploid progenitors. Thus “transcriptome downsizing” occurs more rapidly than genome downsizing. The contributions of homoeologous loci to overall expression were measured in over 5,000 genes for which polymorphisms discriminated diploid parent alleles. Both homoeologues were expressed in nearly 90% of these genes, indicating that absolute silencing is rare, as in other species. However, the frequency of silencing varied significantly by dosage response. Extreme dosage responses in either direction were accompanied by higher rates of silencing.
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1 - Cornell University, Department of Plant Biology, 412 Mann Library Building, Ithaca, NY, 14853-5908, USA
2 - Cornell University, Department of Plant Biology, L.H. Bailey Hortorium, 412 Mann Library Building, Ithaca,, New York, 14853-5908, USA
Presentation Type: Oral Paper:Papers for Sections
Location: 556A/Convention Center
Date: Monday, August 2nd, 2010
Time: 9:00 AM