- Library Home /
- Search Collections /
- Open Collections /
- Browse Collections /
- UBC Research Data /
- The sunflower (Helianthus annuusL.) genome reflects...
Open Collections
UBC Research Data
The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements Staton, S. Evan; Bakken, Bradley H.; Blackman, Benjamin K.; Chapman, Mark A.; Kane, Nolan C.; Tang, Shunxue; Ungerer, Mark C.; Knapp, Steven J.; Rieseberg, Loren H.; Burke, John M.
Description
<b>Abstract</b><br/><section data-lang="en" id="section-1-en" lang="en">
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (<i>Helianthus annuus</i> L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing <i>Gypsy</i> LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.</p> </section>
Item Metadata
Title |
The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements
|
Creator | |
Date Issued |
2021-05-19
|
Description |
<b>Abstract</b><br/><section data-lang="en" id="section-1-en" lang="en">
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (<i>Helianthus annuus</i> L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing <i>Gypsy</i> LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.</p> </section> |
Subject | |
Type | |
Notes |
Dryad version number: 4</p> Version status: submitted</p> Dryad curation status: Published</p> Sharing link: https://datadryad.org/stash/share/T-jofQQCw8lfXR8Ou6Fm4VjgNazMOxaxYjPfKXWa9gw</p> Storage size: 499193301</p> Visibility: public</p> |
Date Available |
2020-09-21
|
Provider |
University of British Columbia Library
|
License |
This dataset is made available under a Creative Commons CC0 license with the following additional/modified terms and conditions: CC0 Waiver
|
DOI |
10.14288/1.0397531
|
URI | |
Publisher DOI | |
Grant Funding Agency |
National Science Foundation*; National Science Foundation*; National Institute of Food and Agriculture
|
Rights URI | |
Aggregated Source Repository |
Dataverse
|
Item Media
Item Citations and Data
Licence
This dataset is made available under a Creative Commons CC0 license with the following additional/modified terms and conditions: CC0 Waiver