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The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements

The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements
The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements
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 (Helianthus annuus 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 Gypsy 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.
transposable elements, chromodomain, helianthus annuus, asteraceae, ltr retrotransposon, genome evolution
0960-7412
142-153
Staton, S. Evan
c76ddf61-c677-47a6-88b3-f65786fd2c21
Bakken, Bradley H.
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Blackman, Benjamin K.
f6604c85-03a8-4516-8c78-00bf47c79d41
Chapman, Mark A.
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Kane, Nolan C.
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Tang, Shunxue
71c2474e-92b9-4814-bcbf-e7b8dec812a5
Ungerer, Mark C.
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Knapp, Steven J.
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Rieseberg, Loren H.
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Burke, John M.
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Staton, S. Evan
c76ddf61-c677-47a6-88b3-f65786fd2c21
Bakken, Bradley H.
6d4de659-fb70-4d62-9dcf-54d27d1db04e
Blackman, Benjamin K.
f6604c85-03a8-4516-8c78-00bf47c79d41
Chapman, Mark A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Kane, Nolan C.
64a24b15-aa9e-43ea-bce7-cb30f760c62f
Tang, Shunxue
71c2474e-92b9-4814-bcbf-e7b8dec812a5
Ungerer, Mark C.
24d46d9e-b292-46ab-a252-c572b9d1d188
Knapp, Steven J.
1f90f391-2672-4efd-a1cf-5e03327f54d4
Rieseberg, Loren H.
7919a08a-3233-4b08-b31b-ab0dbb27f830
Burke, John M.
f74dabe1-09b5-4473-9860-6eb876588d09

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. and Burke, John M. (2012) The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. The Plant Journal, 72 (1), 142-153. (doi:10.1111/j.1365-313X.2012.05072.x).

Record type: Article

Abstract

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 (Helianthus annuus 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 Gypsy 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.

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More information

Published date: July 2012
Additional Information: Times Cited: 1
Keywords: transposable elements, chromodomain, helianthus annuus, asteraceae, ltr retrotransposon, genome evolution
Organisations: Centre for Biological Sciences

Identifiers

Local EPrints ID: 352755
URI: http://eprints.soton.ac.uk/id/eprint/352755
ISSN: 0960-7412
PURE UUID: 7a8ef6f9-b7d8-4f58-97cc-8394564841df
ORCID for Mark A. Chapman: ORCID iD orcid.org/0000-0002-7151-723X

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Date deposited: 20 May 2013 14:35
Last modified: 15 Mar 2024 03:46

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Contributors

Author: S. Evan Staton
Author: Bradley H. Bakken
Author: Benjamin K. Blackman
Author: Mark A. Chapman ORCID iD
Author: Nolan C. Kane
Author: Shunxue Tang
Author: Mark C. Ungerer
Author: Steven J. Knapp
Author: Loren H. Rieseberg
Author: John M. Burke

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