Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea

Transposable elements (TEs) make up over half of Brassica genomes, yet their role in evolution and gene regulation has remained elusive. In our new study, we developed a graph-based clustering approach to redefine TE families in Brassica rapa and B. oleracea, two closely related but morphologically diverse crops. We discovered that LTR retrotransposons were major drivers of speciation, and that TE expression patterns can be predicted by distinct features such as DNA methylation. By integrating gene synteny, we showed that TEs are enriched near genes linked to reproduction, development, stress responses, and transcriptional regulation. Importantly, floral genes located close to TEs displayed greater expression variability, revealing TEs’ potential as regulators of key traits. These findings shed light on how TEs shape genome evolution in crops and highlight their untapped potential for breeding and genome engineering.

Po-Xing Zheng, Chia-Ying Ko, Jheng-Yan Ou, Andrea Zuccolo, Yao-Cheng Lin (2025) Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea The Plant Journal, https://doi.org/10.1111/tpj.70452