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

Zheng P.-X. Ko C.-Y. Ou J.-Y. Zuccolo A. Lin Y.-C.
September 2025 John Wiley and Sons Inc

Plant Journal
2025 #123 Issue 5

Transposable elements (TEs) significantly influence genomic diversity and gene regulation in plants. Brassica rapa and B. oleracea, with their distinct domestication histories, offer excellent models to explore TE dynamics. Here, we developed a refined TE classification method and systematically analyzed TEs across 12 B. rapa and B. oleracea genomes, identifying 1878 TE families. Approximately half (49.5%) of these TE families were shared between the two species, reflecting a common evolutionary origin, whereas species-specific expansions, particularly among long-terminal repeat (LTR) retrotransposons, underscore their roles in genomic differentiation. We notably characterized a heat-responsive Ty1-copia family (Copia0035) in B. oleracea roots, distinguished by low GC content and the absence of CG and CHG methylation motifs, sharing regulatory similarities with the Arabidopsis heat-induced ONSEN element. Syntenic analyses of gene-TE associations highlighted significant intraspecies TE insertion variability, with more accession-specific insertions in B. rapa and more conserved insertions, often associated with distinct morphotypes in B. oleracea. Gene ontology enrichment indicated TE involvement in developmental, reproductive, and stress response pathways. Transcriptome analysis across diverse accessions revealed that genes proximal to TEs, particularly those regulating floral development and flowering time, exhibit increased expression variability. These findings advance our understanding of TE-mediated genome evolution in Brassica species and underscore their potential utility in breeding and genome engineering strategies for crop improvement.

Brassica , epigenetic regulation , gene expression variability , genome evolution , heat stress response , transposable elements

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Biotechnology Center of Southern Taiwan, Academia Sinica, Tainan, 711010, Taiwan
Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115201, Taiwan
Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701401, Taiwan
Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Institute of Crop Science, Scuola Superiore SantAnna, Pisa, 56127, Italy
Manash Kozybayev North Kazakhstan University, Petropavl, 150000, Kazakhstan
Biotechnology Center, National Chung Hsing University, Taichung, 402202, Taiwan
Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, 804201, Taiwan

Biotechnology Center of Southern Taiwan
Agricultural Biotechnology Research Center
Institute of Tropical Plant Sciences and Microbiology
Center for Desert Agriculture (CDA)
Institute of Crop Science
Manash Kozybayev North Kazakhstan University
Biotechnology Center
Department of Marine Biotechnology and Resources

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