Abstract Detail

Functional Genetics/Genomics

Di Santo, Lionel [1], Kittilson, Jeffrey [1], Dlugosch, Katrina [2], Barker, Michael [2], Hamilton, Jill [1].

Niche evolution following whole genome duplication.

Quantifying the role whole genome duplications (WGD) have played in the evolution of the ecological niche is a fundamental aim of evolutionary biology. Following whole genome duplication, there is good evidence that polyploids diverge ecologically from their diploid progenitors, exhibiting an increased rate of niche evolution relative to diploids. However, despite extensive evidence for the important role of WGD in niche divergence, few studies have assessed how ploidy-level genetic changes have contributed to niche evolution. This study aims to fill this gap quantifying the relative response of duplicate genes associated with different ancestral sub-genomes (homeologs) to selection across environments. Following whole genome duplication, functional variation may evolve via neo or sub-functionalization, enabling rapid adaptation to changing environments. In this study, we use Prairie Smoke (Geum triflorum Pursh.), a perennial allohexaploid whose distribution spans a range of extreme environments, to quantify different mechanisms of selection contributing to sub-genome evolution. We extracted and sequenced RNA from leaf tissue of G. triflorum sourced from three different environments all grown together under common environmental conditions and its two diploid progenitors (Coluria geoides and Waldsteinia geoides). Transcriptomes of all three species were assembled de novo using SoapDeNovo-Trans and homoeologs were identified using a custom pipeline. We quantified the ratio of synonymous to nonsynonymous mutations (Ka/Ks) for all homeologs within and across environments, predicting that (i) gene duplicates undergoing neofunctionalization would be under positive selection (Ka/Ks>1), (ii) genes undergoing subfunctionalization would exhibit evidence of negative (purifying) selection (Ka/Ks<1), and (iii) gene duplicates restricted to one environment would indicate candidates for nonfunctionalization via silencing. These data will be key to understanding the role ploidy-level changes have played in niche evolution; including the generation, maintenance or loss of genetic variation needed for rapid evolution.

1 - North Dakota State University, Department of Biological Sciences, PO Box 6050, Fargo, ND, 58108-6050, United States
2 - University of Arizona, Department of Ecology & Evolutionary Biology, 1041 E. Lowell St., Biological Sciences West, Tucson, AZ, 85721, USA
3 - North Dakota State University, Department of Biological Sciences, PO Box 6050, Fargo, ND, 58108-6050, United States

Keywords:
niche divergence
polyploid evolution
homeologs evolution
Whole genome duplication.

Presentation Type: Oral Paper
Session: FG1, Functional Genetics and Genomics
Location: San Luis 1/Starr Pass
Date: Monday, July 29th, 2019
Time: 2:30 PM
Number: FG1003
Abstract ID:138
Candidate for Awards:None