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 chloroplast-replicating 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.

在整个生物系统中，突变率变化的数量级不同，对于简单的基因组，突变率更高。最简单的已知基因组对应于类病毒，即由数百个碱基的环状非编码RNA构成的亚病毒植物复制子。先前的研究表明，菊花的叶绿素斑驳类病毒（叶绿体复制类病毒）的突变率极高。但是，这是否是类病毒的一般特征仍不清楚。在这里，我们使用了高保真超深测序来确定两个类病毒的共同宿主（茄子）中的突变率，每个类都代表一个家族：叶绿体茄子潜在类病毒（ELVd，Avsunviroidae）和核马铃薯纺锤形块茎类病毒（PSTVd，类病毒科））。这表明ELVd中的突变频率高于PSTVd中的突变频率，并且产生的突变类型存在明显差异。根据测序运行情况，使用致死突变方法在体内进行量化的自发突变发生率，对于ELVd为1/1000至1/800，对于PSTVd为1/7000至1/3800。这些结果表明，极高的变异性是叶绿体类病毒的一个共同特征，而PSTVd和潜在的其他核类病毒的突变率则明显低于某些RNA病毒。