Abstract Detail

Population Genetics/Genomics

Hofford, Nate [1], Motley, M'Kayla [2], MacNeill, Bryan [3], Deb, Sontosh [4], Adhikari, Bishnu [3], Busby, Andrew [5], McLaughlin, Susan [6], Oldham, Fae [6], McKain, Michael [7].

Johnsongrass jumping genes: Population-level variation in transposable element content and correlations with environmental characteristics.

Transposable elements (TEs) are mobile DNA sequences capable of changing position and copy number within the genome. These elements make up a large portion of plant genomes and through their transposition increase mutation rate and can alter gene expression patterns. To prevent overproliferation, TEs are regulated through epigenetic mechanisms which in turn can be altered by changes in the environment. Because of (1) their potential to create genomic novelty and (2) linkage between their regulatory mechanisms and environmental changes, TEs have been proposed as a mechanism to explain the adaptive potential of invasive populations. Most research has focused on elucidating the phenotypic and ecological strategies associated with invasiveness. However, relatively little attention has been paid to understanding the genomic basis of adaptation in the face of limited diversity. In this study, we investigate the relationship between TE content and environmental variables in populations of Johnsongrass (Sorghum halepense), an invasive grass throughout the southern/middle US. Our study has two primary aims: (1) Characterize variation in the TE composition of Johnsongrass genomes across its US invasive range and (2) assess environmental/geographic correlates of TE richness, diversity, and genomic proportion. We collected 312 live plants from 59 populations across the invasive US range of Johnsongrass, sampling at least three individuals per population. Whole genome shotgun sequences at a coverage of ~1.2x (2 Gb data for ~1.7 Gb genome) were generated for each sample with Illumina. A custom computational pipeline was used to quality assess and remove contamination from all sequence reads before transposable elements were quantified using Transposome. We characterized the environmental conditions at each site by extracting BioClim variables at the 0.5 arc min resolution. Genome size estimation from a subset of our samples was carried out using flow cytometry to ascribe the absolute size of the TE proportion of these genomes. We then assessed the relationship between these environmental variables, TE content and genome size using partial linear regression. This work represents the first population-level assessment of transposable element variation within a broadly distributed invasive species. Future studies should address the adaptive relevance of this variation to identify the exact genomic mechanisms of invasion success.

1 - University Of Alabama, Biology, 530 18th Street, Unit 206, Tuscaloosa, AL, 35401, United States
2 - University Of Alabama, Box 870118, Box 870118, Tuscaloosa, AL, 35487, United States
3 - University Of Alabama , Department Of Biology, Science And Engineering Complex, 1325 Hackberry Ln, Tuiscaloosa, AL, 35401, United States
4 - The University of Alabama, 405 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, United States
5 - The University of Alabama, Biological Sciences, Science And Engineering Complex, 1325 Hackberry Ln, Tus, AL, 35401, USA
6 - The University of Alabama, Biological Sciences, Science And Engineering Complex, 1325 Hackberry Ln, Tuscaloosa, AL, 35401, United States
7 - University Of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, United States

transposable elements
invasive species
intraspecific variation
genome size variation
environmental variation.

Presentation Type: Oral Paper
Number: PGG2007
Abstract ID:902
Candidate for Awards:Margaret Menzel Award

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