| Summary: | <ul>
<li>C<sub>3</sub>-C<sub>4</sub> intermediate photosynthesis has evolved at least five times convergently in the Brassicaceae, despite this family lacking <em>bona fide</em> C<sub>4</sub> species. The establishment of this carbon concentrating mechanism is known to require a complex suite of ultrastructural modifications, as well as changes in spatial expression patterns, which are both thought to be underpinned by a reconfiguration of existing gene-regulatory networks. However, to date, the mechanisms which underpin the reconfiguration of these gene networks are largely unknown.</li>
<li>In this study, we used a pan-genomic association approach to identify genomic features that could confer differential gene expression towards the C<sub>3</sub>-C<sub>4</sub> intermediate state by analysing eight C<sub>3</sub> species and seven C<sub>3</sub>-C<sub>4</sub> species from five independent origins in the Brassicaceae.</li>
<li>We found a strong correlation between transposable element (TE) insertions in <em>cis</em>-regulatory regions and C<sub>3</sub>-C<sub>4</sub> intermediacy. Specifically, our study revealed 113 gene models in which the presence of a TE within a gene correlates with C<sub>3</sub>-C<sub>4</sub> intermediate photosynthesis. In this set, genes involved in the photorespiratory glycine shuttle are enriched, including the glycine decarboxylase P-protein whose expression domain undergoes a spatial shift during the transition to C<sub>3</sub>-C<sub>4</sub> photosynthesis. When further interrogating this gene, we discovered independent TE insertions in its upstream region which we conclude to be responsible for causing the spatial shift in <em>GLDP1</em> gene expression.</li>
<li>Our findings hint at a pivotal role of TEs in the evolution of C<sub>3</sub>-C<sub>4</sub> intermediacy, especially in mediating differential spatial gene expression.</li>
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