Abstract Detail

Comparative Genomics/Transcriptomics

Coate, Jeremy [1], Doyle, Jeff [2].

The Effect of Polyploidy on Transcriptome Size and Dosage Responses in Natural and Synthetic Polyploids.

“Genome downsizing” is a commonly observed phenomenon in polyploid evolution, in which the size of the polyploid’s genome is smaller than would be expected given the genome size of its diploid progenitor(s). Much less is known, however, about the response of the overall transcriptome to polyploidy. We have shown previously that Glycine dolichocarpa, an allopolyploid (2n = 80) relative of soybean (G. max, 2n = 40) shows “transcriptome downsizing”, having a leaf transcriptome that is around 1.4x the size of its two diploid progenitors (i.e., 0.7x per genome), both of which have similar transcriptome sizes. We have extended this observation to the leaf transcriptomes of other Glycine allopolyploid species, and also to the root transcriptome of G. dolichocarpa, all of which show an approximately 1.5x larger size in polyploids. Because these natural Glycine allopolyploid species are all several hundred thousand years old, it is unclear whether this downsizing is an immediate effect of allopolyploidy, or a function of parallel divergence in these independently formed polyploids. To explore the earliest stages of polyploidy, we have measured transcriptome size in a synthetic Arabidopsis thaliana polyploid. As in Glycine, the Arabidopsis autotetraploid exhibits leaf transcriptome downsizing (0.8-0.9x expression per genome). Estimates of transcriptome size per cell are complicated by the fact that, unlike in Glycine, Arabidopsis leaf tissue includes endopolyploid cells, and the degree of endopolyploidy varies between accessions. Allowing for endopolyploidy, average transcriptome size on a per cell basis is only about 1.1-1.2x larger in the tetraploids than in their diploid parents. In both Glycine and Arabidopsis approximately 20% of genes are dosage compensated (no change in expression following a doubling of copy number), and these are enriched for genes functioning in translation. Approximately 20% of genes in Glycine and 34% of genes in Arabidopsis show a 1:1 dosage effect (a doubling of transcription following a doubling of copy number), and these are enriched for GO terms relating to signal transduction and transport. The fact that a doubling of gene content does not produce a doubling of transcription, even in the first generations after genome duplication, indicates that less than doubled gene expression is an immediate effect of genome duplication, and perhaps an emergent effect of polyploidy.

1 - Reed College, Plant Biology, 3203 SE Woodstock Blvd., Portland, OR, 97202, USA
2 - Cornell University, 412 Mann Library Building, ITHACA, NY, 14853-4301, USA

Keywords:
Polyploidy
Transcriptome
Gene Dosage Response.

Presentation Type: Oral Paper
Session: 10, Comparative Genomics and Transcriptomics
Location: Fort Worth Ballroom 5/Omni Hotel
Date: Monday, June 26th, 2017
Time: 2:30 PM
Number: 10005
Abstract ID:112
Candidate for Awards:None