# Dynamics of transposable elements in the hexaploid wheat genome

Conference Jacques Monod

Evolutionary and ecological genomics of polyploidy in plants
Sept 15th 2025 - Roscoff
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4,5%

3,0%

1,9%

1,6%

0,9%

0,7%

0,1%

3,0%

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CDS divergence
<figure><img src="image_8.png" /><figcaption>100 kb</figcaption></figure>

<figure><img src="image_9.png" /><figcaption>CDSs: ~1% of seq</figcaption></figure>

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~5000 wheat
TE sequences

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classification

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~500 (sub)families
with classification

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Importance of TE classification...

<figure><img src="image_20.png" /><figcaption>estimated date
of insertions</figcaption></figure>

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<figure><img src="image_21.png" /><figcaption>The TE turnover</figcaption></figure>
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* Abundant families are the same on A-B-D

* 0 family specific to 1 subgenome

* Similar copy numbers of each family betw A-B-D

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* TE inserted in the diploids

* rare insertions in tetraploid AABB
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<table><thead><tr><th rowspan="2">FAMILY</th><th colspan="3">copy number</th></tr><tr><th>A</th><th>B</th><th>D</th></tr></thead><tbody><tr><td>RLG_famc5</td><td>50991</td><td>45056</td><td>36241</td></tr><tr><td>RLG_famc6</td><td>25026</td><td>30352</td><td>22616</td></tr><tr><td>RLG_famc7</td><td>54675</td><td>31771</td><td>23264</td></tr><tr><td>RLG_famc8</td><td>18021</td><td>13226</td><td>14734</td></tr><tr><td>RLG_famc9</td><td>14913</td><td>19001</td><td>15596</td></tr><tr><td>RLG_famc10</td><td>12995</td><td>12470</td><td>14311</td></tr><tr><td>RLG_famc11</td><td>29185</td><td>18187</td><td>22347</td></tr><tr><td>RLG_famc12</td><td>9009</td><td>9459</td><td>11960</td></tr><tr><td>RLG_famc13</td><td>19810</td><td>18342</td><td>19276</td></tr><tr><td>RLG_famc14</td><td>6942</td><td>7710</td><td>9611</td></tr><tr><td>RLG_famc15</td><td>9645</td><td>11705</td><td>4173</td></tr><tr><td>RLG_famc16</td><td>1360</td><td>950</td><td>1543</td></tr><tr><td>RLG_famc17</td><td>6439</td><td>6835</td><td>6153</td></tr><tr><td>RLG_famc18</td><td>426</td><td>533</td><td>414</td></tr><tr><td>RLG_famc19</td><td>6281</td><td>6756</td><td>8100</td></tr><tr><td>RLG_famc20</td><td>4724</td><td>3747</td><td>3393</td></tr><tr><td>RLG_famc21</td><td>698</td><td>1128</td><td>860</td></tr><tr><td>RLG_famc22</td><td>641</td><td>712</td><td>626</td></tr><tr><td>RLG_famc23</td><td>834</td><td>1025</td><td>761</td></tr><tr><td>RLG_famc24</td><td>553</td><td>1860</td><td>985</td></tr><tr><td>RLG_famc25</td><td>1295</td><td>3247</td><td>1600</td></tr><tr><td>RLG_famc26</td><td>653</td><td>830</td><td>511</td></tr><tr><td>RLG_famc27</td><td>179</td><td>935</td><td>169</td></tr><tr><td>RLG_famc28</td><td>21</td><td>20</td><td>25</td></tr><tr><td>RLG_famc29</td><td>669</td><td>804</td><td>686</td></tr><tr><td>RLG_famc30</td><td>1562</td><td>2121</td><td>4439</td></tr><tr><td>RLG_famc31</td><td>260</td><td>358</td><td>375</td></tr><tr><td>RLG_famc32</td><td>2001</td><td>1951</td><td>962</td></tr><tr><td>RLG_famc33</td><td>654</td><td>677</td><td>474</td></tr><tr><td>RLG_famc34</td><td>101</td><td>119</td><td>133</td></tr><tr><td>RLG_famc35</td><td>919</td><td>1359</td><td>708</td></tr><tr><td>RLG_famc36</td><td>661</td><td>1095</td><td>339</td></tr><tr><td>RLG_famc37</td><td>1189</td><td>1092</td><td>1072</td></tr><tr><td>RLG_famc38</td><td>18</td><td>41</td><td>22</td></tr></tbody></table>
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Log2 fold change

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<figure><img src="image_28.png" /><figcaption>➤ Enrichment in gene promoters is conserved betw A-B-D</figcaption></figure>
❖ Whole Genome Alignments

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<figure><img src="image_30.png" /><figcaption>* T. aestivum
13 assembled genome seqs</figcaption></figure>

<figure><img src="image_31.png" /><figcaption>* T. durum</figcaption></figure>

* T. dicoccoides

<figure><img src="image_32.png" /><figcaption>* T. urartu</figcaption></figure>

<figure><img src="image_33.png" /><figcaption>* Ae. tauschii</figcaption></figure>
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versus

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versus

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❖ Counting novel insertions
~4,000-13,000 / subgenome

Query

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Ref

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<table><thead><tr><th colspan="2">% variable</th></tr><tr><th>Query</th><th>Ref</th></tr></thead><tbody><tr><td>34</td><td>32%</td></tr><tr><td>13</td><td>10%</td></tr><tr><td>7</td><td>7%</td></tr><tr><td>6</td><td>6%</td></tr></tbody></table>

* No genome contraction/expansion

* No impact of polyploidy on TE activity

* ~ All families were active recently
#novel TE insertions

20 most abundant families

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ClariTeRep

TREP

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Conclusions

* TE turnover without expansion/contraction

* ~All families were active recently

* Constant transposition rate

* No impact of polyploidy

* Transposition not a response to stress...

* ...rather, a highly regulated process

* Equilibrium model of evolution (as opposed to the TE-burst model)

* Structural function of TEs under constraint?
❖ Acknowledgments

❖ GDEC

Nathan Papon
Romain De Oliveira
Josquin Daron

Thomas Wicker, UZH Zurich
Heidrun Gundlach, PGSB Munich

Int. Wheat Genome Seq. Consortium

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MÉSOCENTRE
Université Clermont Auvergne