Organization and evolution of transposable elements along the bread wheat chromosome 3B

Area of Science:

• Genomics
• Plant Biology
• Evolutionary Biology

Background:

• The bread wheat genome (17 Gb) is characterized by extensive transposable element (TE) proliferation and polyploidization.
• A reference sequence of wheat chromosome 3B enables high-resolution analysis of TE impact on genome structure and evolution.

Purpose of the Study:

• To develop an automated workflow (CLARI-TE) for transposable element (TE) modeling in complex plant genomes.
• To investigate the impact of TEs on the structure and evolution of the wheat chromosome 3B.

Main Methods:

• Automated TE modeling using the CLARI-TE workflow.
• Delineation of intact, fragmented, and nested TEs on the wheat chromosome 3B pseudomolecule.
• Analysis of TE activity, elimination, and association with genomic features.

Main Results:

• Precisely mapped 56,488 intact and 196,391 fragmented TEs, comprising 85% of the 3B chromosome sequence.
• Identified major TE bursts between 1-3 million years ago, with recent TE silencing.
• Revealed accelerated TE elimination in high-recombination regions and linked CACTA elements to gene duplication and potential adaptation.

Conclusions:

• Accurate TE modeling is crucial for understanding dynamics in complex, polyploid genomes.
• TEs, particularly CACTAs, significantly influence wheat chromosome structure, gene duplication, and adaptation.