Low ribosomal RNA genes copy number provoke genomic instability and chromosomal segment duplication events that modify global gene expression and plant-pathogen response

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Picart-Picolo, Ariadna
Grob, Stefan
Picault, Nathalie
Franek, Michal
Halter, Thierry
Maier, Tom
Llauro, Christel
Jobet, Edouard
Zhang, Panpan
Vijayapalani, Paramasivan
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Baum, Thomas
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Plant Pathology and Microbiology
The Department of Plant Pathology and Microbiology and the Department of Entomology officially merged as of September 1, 2022. The new department is known as the Department of Plant Pathology, Entomology, and Microbiology (PPEM). The overall mission of the Department is to benefit society through research, teaching, and extension activities that improve pest management and prevent disease. Collectively, the Department consists of about 100 faculty, staff, and students who are engaged in research, teaching, and extension activities that are central to the mission of the College of Agriculture and Life Sciences. The Department possesses state-of-the-art research and teaching facilities in the Advanced Research and Teaching Building and in Science II. In addition, research and extension activities are performed off-campus at the Field Extension Education Laboratory, the Horticulture Station, the Agriculture Engineering/Agronomy Farm, and several Research and Demonstration Farms located around the state. Furthermore, the Department houses the Plant and Insect Diagnostic Clinic, the Iowa Soybean Research Center, the Insect Zoo, and BugGuide. Several USDA-ARS scientists are also affiliated with the Department.
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Among the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA line). Compared to the wild-type Col-0, the 20rDNA line shows several signs of genomic instability, such as variations in 3D genome organization, spontaneous double-strand breaks accumulation, transcriptomic changes, and higher DNA methylation level. Strikingly, using genomic and microscopic approaches, we identified seven large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. As a consequence, more than 600 genes were duplicated, often associated with an increase in their expression level. Among them, we found several upregulated genes 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 we discuss their potential implications on plant genome evolution.


This is a preprint made available through bioRxiv, doi: 10.1101/2020.01.24.917823.

Wed Jan 01 00:00:00 UTC 2020