Abstract Detail

Comparative Genomics/Transcriptomics

McKain, Michael [1], Pienaar, Jason [2], Zudock, Kristina [3], AuBuchon, Taylor [4], Saeidi, Saman [4], Pasquet, Remy [5], Layton, Daniel [6], Welker, Cassiano [7], Art-han, Watchara [8], Traiperm, Paweena [9], McAllister, Chrissy [10], Kellogg, Elizabeth [11].

Transposon diversity and abundance variation as a consequence of climatic variables in Andropogoneae (Poaceae).

Transposable elements (TEs) are a major component of angiosperm genomes. Variation of transposon diversity and abundance are well documented in a number of sequenced genomes and across lineages in a few, well studied taxa. Multiple adaptive hypotheses exist to describe TE variation in genomes, but there is a need to test these hypotheses in a phylogenetic context across a lineage anchored by well-characterized genomes. Here we assembled a data set of 47, low coverage shotgun sequenced Andropogoneae accessions, where we estimated genome size and transposable element abundance for each individual. As part of this study, we demonstrate a bootstrapping method that uses subsets of reads and the software Transposome to quickly and accurately depict the transposon landscape of low-coverage sequenced genomes. Using voucher information, we gathered data on the sampling location (altitude, longitude, latitude) and bioclimatic variables for each accession, which we combined with ploidy estimation and duration (annual vs. herbaceous perennial). Using a well-resolved plastome phylogeny and a suite of phylogenetic comparative methods with an Ornstein-Uhlenbeck process, we tested all combinations of variables as alternative hypotheses for factors that influence the adaptive landscape for the abundance of each transposable element superfamily. We used Aikake Information Criteria to select amongst the various adaptive and neutral evolution hypotheses (modeled as a Brownian motion on the phylogeny). We find that only microsatellites evolve neutrally, whereas the larger satellites are constrained by stabilizing selection around a single, global optimum. Adaptive landscapes of the remaining transposable elements are all affected by residual genome size (genome size minus all transposable elements) in combination with either bioclimatic variable 3 (isothermality) for Copia and Gypsy retroelements, helitrons and MuDR, or life history for MuDR and retroelements (where perennials have higher TE abundance). Most bioclimatic variables that affect TEs involve some aspect of temperature. For Andropogoneae, evidence supports the hypothesis that temperature stability is the main environmental determinant of TE abundance, where abundance is higher in more stable temperature environments.

1 - The University of Alabama, Biological Sciences, 300 Hackberry Lane, Tuscaloosa, Alabama, 35487, United States
2 - The University of Alabama, Biological Sciences, 300 Hackberry Lane, Box 870344, Tuscaloosa, Alabama, 35487, United States
3 - Washington University in St. Louis, Biology, Campus Box 1137, St. Louis, MO, 63130
4 - Donald Danforth Plant Science Center, 975 N Warson, St Louis, MO, 63132, United States
5 - Unité de Recherche Institut de Recherche pour le Développement , Laboratoire Évolution, Génomes et Spéciation, Orsay, France
6 -
7 - Rua Sete De Setembro, 243, Esteio, RS, 93285280, Brazil
8 - Kew Gardens, Comparative Plant & Fungal Biology, London Borough of Richmond upon Thames, UK
9 - Mahidol University, Department of Plant Science, Bangkok, Thailand
10 - 1 Maybeck Place, Principia College, Elsah, IL, 62028, United States
11 - Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, United States

Keywords:
Andropogoneae
Poaceae
genome evolution
transposable elements
bioclim.

Presentation Type: Oral Paper
Session: 25, Comparative Genomics and Transcriptomics II
Location: 102/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 4:45 PM
Number: 25015
Abstract ID:942
Candidate for Awards:Margaret Menzel Award