Abstract Detail

Genomics / Proteomics

Tiley, George [1], Ane, Cecile [2], Burleigh, Gordon [3].

Heterogeneity in loss rates following whole genome duplication across land plants.

Whole genome duplications (WGDs) have helped shape the genomes of land plants, and recent evidence suggests that all angiosperms have had at least two WGDs. In plants, WGDs often are followed by rapid fractionation, in which many homeologous gene copies are lost, diminishing evidence of WGDs. Thus, it can be extremely difficult to identify, let alone characterize, ancient WGDs. In this study, we use a new maximum likelihood estimator of gene duplication and loss rates from gene family copy numbers that explicitly accounts for WGD events. This provides a robust statistical framework to test if we can identify evidence of ancient WGDs in land plants from gene count data and estimate the fraction of new genes copies that are retained following a WGD. We identified evidence of most putative ancient WGDs in land plants. The genome fractionation rates vary tremendously among ancient WGDs. Analyses of WGDs within Brassicales also indicate that background single gene duplication and loss rates vary across land plants and different sets of genes have different probabilities of being retained following a WGD. Although our analyses are largely robust to errors in background duplication and loss rates and the choice of priors, it appears to be extremely difficult to detect the most ancient putative WGDs using only gene count data. Still, our analyses suggest that we should carefully reevaluate evidence for some ancient plant WGD hypotheses.

1 - University of Florida, Biology, Gainesville, FL, 32611, USA
2 - University of Wisconsin, Statistics/Botany, Madison, WI, 53706, USA
3 - University Of Florida, P.O. Box 118526, Gainesville, FL, 32611, USA

Keywords:
whole genome duplication
gene family evolution
gene duplication.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PGP006
Abstract ID:633
Candidate for Awards:Genetics Section Poster Award