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Abstract Detail



Genomics / Proteomics

Visger, Clayton [1], Wong, Gane Ka-Shu [2], Soltis, Pamela S. [3], Soltis, Douglas [4].

Quantifying transcriptome-wide levels of gene expression following autopolyploidy in Tolmiea (Saxifragaceae).

Research on the genetic consequences of whole-genome duplication has historically focused on allopolyploidy, to the near exclusion of autopolyploidy, reflecting the traditional view that autopolyploidy is rare and of limited evolutionary importance. However, there is increasing recognition that autopolyploidy is a frequent and major evolutionary force, especially in certain clades. While autopolyploidy can serve as an instant speciation mechanism, we know almost nothing about the ecological, genetic, and genomic consequences of this process. The angiosperm genus Tolmiea (Saxifragaceae) represents an excellent evolutionary model for the study of natural autopolyploidy, comprising two species, the autotetraploid T. menziesii (2n = 28) and its diploid progenitor, T. diplomenziesii (2n = 14).
Here we present results of our study of transcriptome-wide gene expression following autopolyploidy in Tolmiea. We used RNAseq to characterize patterns of differential gene expression across multiple populations of diploid and autotetraploid Tolmiea. Individuals collected from 3 populations of each ploidal level were vegetatively propagated and raised in a common garden. We extracted and sequenced four biological replicates of total RNA (leaf tissue) from each individual (24 samples in total). Prior to library preparation, total RNA was spiked with ERCC spike-in standards, which were used downstream to correct for differences in total transcriptome size. Raw reads were mapped to a de novo diploid reference using BowTie2, and DEseq was used to characterize genes as differentially expressed. Differentially expressed loci were binned by inferred ontology and further investigated for over/under-representation. Using this approach, we report on the differences in total transcriptome size, the proportion of the transcriptome expressed additively versus non-additively (dosage-insensitive), and any patterning with respect to ontology.


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1 - University of Florida, Biology and Florida Museum of Natural History, Gainesville, Fl, 32611, USA
2 - University of Alberta, Biological Sciences; Medicine (Gastroenterology), CW405 Biological Sciences, Edmonton, AB, T6G 2E9, Canada
3 - University Of Florida, Florida Museum Of Natural History, PO Box 117800, Gainesville, FL, 32611-7800, USA, 352/273-1964
4 - University of Florida, Florida Museum of Natural History, 1659 Museum Road, Dickinson Hall, Gainesville, FL, 32611, USA

Keywords:
Polyploidy
autopolyploidy
gene expression
RNA-Seq.

Presentation Type: Oral Paper:Papers for Topics
Session: 39
Location: Salon 19/20/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 11:00 AM
Number: 39008
Abstract ID:836
Candidate for Awards:Margaret Menzel Award


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