TY  - JOUR
A1  - Picart-Picolo, Ariadna
A1  - Grob, Stefan
A1  - Picault, Nathalie
A1  - Franek, Michal
A1  - Llauro, Christel
A1  - Halter, Thierry
A1  - Maier, Tom R.
A1  - Jobet, Edouard
A1  - Descombin, Julie
A1  - Zhang, Panpan
A1  - Paramasivan, Vijayapalani
A1  - Baum, Thomas J.
A1  - Navarro, Lionel
A1  - Dvořáčková, Martina
A1  - Mirouze, Marie
A1  - Pontvianne, Frédéric
T1  - Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
Y1  - 2020/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1583 
EP  - 1592 
DO  - 10.1101/gr.261586.120 
VL  - 30 
IS  - 11 
UR  - http://genome.cshlp.org/content/30/11/1583.abstract 
N2  - Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes. 
ER  -