Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response

Area of Science:

• Plant genetics
• Genomics
• Evolutionary biology

Background:

• Rapid plant genome evolution is essential for adaptation.
• Chromosomal rearrangements and gene copy number variation (CNV) drive genome evolution but typically require many generations.
• The chromatin assembly factor 1 (CAF1) complex plays a role in genome stability.

Purpose of the Study:

• To investigate rapid genome structure changes in Arabidopsis thaliana.
• To explore the role of ribosomal RNA (rRNA) gene loss in driving these changes.
• To understand the impact of large tandem duplications in direct orientation (TDDOs) on genome organization, gene expression, and plant immunity.

Main Methods:

• Long-read sequencing
• Microscopic approaches
• Analysis of a 20% rRNA gene copy line (20rDNA line)

Main Results:

• Identified up to 15 independent TDDOs (60 kb to 1.44 Mb) appearing within a few generations.
• TDDOs led to the duplication of hundreds of genes, with duplicated genes accumulating more transcripts.
• The 20rDNA line exhibited hyper-resistance to bacterial and nematode infections, potentially due to duplicated plant-pathogen response genes.
• TDDOs were shown to create gene fusions and truncations.

Conclusions:

• Ribosomal RNA (rRNA) gene loss, coupled with CAF1 mutations, can rapidly induce large tandem duplications (TDDOs) in Arabidopsis thaliana.
• These TDDOs significantly alter genome structure and gene expression in a short evolutionary timeframe.
• The observed genomic changes contribute to enhanced plant defense mechanisms and offer insights into plant genome evolution.