Satellite RNAs (satRNAs) are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. While much is known about the replication and pathogenicity of satRNAs, their origin remains a mystery. A previous study has reported de novo emergence of Cucumber mosaic virus (CMV) satRNAs on serial passaging plants with CMV helper virus infection. Two main origins of satRNA have been suggested: the genome of the helper virus or that of the host plant.

To explore the origin of CMV satRNA, Prof. GUO Huishan’s group at Institute of Microbiology of Chinese Academy of Sciences cooperated with WANG Mingbo from Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Australia. The researchers constructed a fusion transgene containing the CMV satRNA sequence, and found that only the CMV SatRNA sequence region was methylated in Nicotiana tabacum plants. This indicates that the satRNA sequence is subject to 24-nt small RNA (sRNA)-directed DNA methylation. 24-nt sRNAs as well as multiple genomic DNA fragments with sequence homology to satRNA were detected in Nicotiana plants, which suggests that the Nicotiana genome contains satRNA-like repetitive DNA sequences. 

Bioinformatic analysis of sRNA libraries from CMV-infected and wild type Nicotiana plants showed that the number of matching sRNAs was generally increased in the CMV-infected sample compared to the wild type sample, and the majority of them likely derived from highly repetitive region. Some satRNAs matching small interfering RNA (siRNA) sequences aligned with several regions of the satRNA genome, suggesting the possible existence of long stretches of satRNA-like sequences in the Nicotiana genome. 

The study points to a host genome origin for CMV satRNAs, and suggests novel approach of using small RNA sequences for finding the origin of other satRNAs. The results were published in PLoS Genetics. 

The work was supported by grants from National Program on Key Basic Research Project of China and the Natural Science Foundation of China.