Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing

6533b86dfe1ef96bd12ca931

RESEARCH PRODUCT

Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing

Rafael Sanjuán Sonia Delgado Selma Gago-zachert Selma Gago-zachert Ricardo Flores Vicente Sentandreu Amparo López-carrasco Cristina Ballesteros

subject

0301 basic medicine Mutation rate Chloroplasts Viroid viruses Pospiviroidae Artificial Gene Amplification and Extension Plant Science Self-Cleavage Virus Replication Biochemistry Polymerase Chain Reaction Genome Database and Informatics Methods Sequencing techniques Ribozyme Nucleic Acids Ribozymes Biology (General)Genetics High-Throughput Nucleotide Sequencing food and beverages RNA sequencing Viroids Enzymes Avsunviroidae Deletion Mutation Viruses Physical Sciences RNA Viral In-Vivo Sequence Analysis Research Article Substitution Mutation Hammerhead Ribozymes QH301-705.5 Materials by Structure Bioinformatics Evolution Materials Science Immunology Plant Pathogens Generation Replication Biology Microbiology 03 medical and health sciences Sequence Motif Analysis Virology Genetics Solanum melongena RNA-Polymerase Molecular Biology Potato spindle tuber viroid Plant Diseases Matter 030102 biochemistry & molecular biology Point mutation Organisms Biology and Life Sciences Proteins RNA Reverse Transcriptase-Polymerase Chain Reaction RC581-607 Plant Pathology biology.organism_classification Virology Research and analysis methods Molecular biology techniques 030104 developmental biology Mutagenesis Oligomers Mutation Enzymology RNA Motif Parasitology Immunologic diseases. Allergy

description

[EN] Mutation rates vary by orders of magnitude across biological systems, being higher for simpler genomes. The simplest known genomes correspond to viroids, subviral plant replicons constituted by circular non-coding RNAs of few hundred bases. Previous work has revealed an extremely high mutation rate for chrysanthemum chlorotic mottle viroid, a chloroplastreplicating viroid. However, whether this is a general feature of viroids remains unclear. Here, we have used high-fidelity ultra-deep sequencing to determine the mutation rate in a common host (eggplant) of two viroids, each representative of one family: the chloroplastic eggplant latent viroid (ELVd, Avsunviroidae) and the nuclear potato spindle tuber viroid (PSTVd, Pospiviroidae). This revealed higher mutation frequencies in ELVd than in PSTVd, as well as marked differences in the types of mutations produced. Rates of spontaneous mutation, quantified in vivo using the lethal mutation method, ranged from 1/1000 to 1/800 for ELVd and from 1/7000 to 1/3800 for PSTVd depending on sequencing run. These results suggest that extremely high mutability is a common feature of chloroplastic viroids, whereas the mutation rates of PSTVd and potentially other nuclear viroids appear significantly lower and closer to those of some RNA viruses.

year	journal	country	edition	language
2017-02-13	PLOS Pathogens

https://doi.org/10.1371/journal.ppat.1006547