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

Area of Science:

• Plant genomics
• Molecular evolution
• Bioinformatics

Background:

• Transposable elements (TEs) are crucial drivers of genomic diversity and gene regulation in plants.
• Brassica rapa and B. oleracea provide valuable models for studying TE dynamics due to their distinct domestication histories.

Purpose of the Study:

• To develop a refined TE classification method and systematically analyze TEs in Brassica genomes.
• To investigate the role of TEs in genomic differentiation and their association with gene regulation and plant traits.

Main Methods:

• Developed a refined TE classification method.
• Systematically analyzed TEs across 12 B. rapa and B. oleracea genomes.
• Performed syntenic and transcriptome analyses to assess gene-TE associations and expression variability.

Main Results:

• Identified 1878 TE families, with 49.5% shared between species, and highlighted species-specific expansions of LTR retrotransposons.
• Characterized a heat-responsive Ty1-copia family (Copia0035) in B. oleracea roots with unique regulatory features.
• Observed significant intraspecies TE insertion variability, with accession-specific insertions in B. rapa and conserved insertions in B. oleracea linked to morphotypes.
• Found TE involvement in developmental, reproductive, and stress response pathways, with proximal genes showing increased expression variability, especially for floral development and flowering time.

Conclusions:

• TEs significantly contribute to genome evolution and differentiation in Brassica species.
• TEs influence gene expression variability, particularly in pathways related to development and stress.
• TEs represent a valuable resource for breeding and genome engineering in crop improvement.