中国番茄上病毒种类多样型－JV－2017

donggua

高通量测序技术对获取病毒种类十分重要，尤其是对一些不常见病毒。2017年3月22日刚接收的Journal of Virology上发表了一篇关于小RNA测序探明中国番茄中病毒种类的研究。
Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing
Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with coldspots and hotspots. Most samples were co-infected by multiple viruses and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data has enabled us to identify several unreported viruses in tomato including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in genus Cytorhabdovirus. Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases.
IMPORTANCE Tomato is an important source of micronutrient in human diet and is extensively consumed in the world. Virus is among the major constrains to tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast evolving biological entities. Here we report the landscape of tomato virome in China, the leading country of tomato production. We identified dozens of viruses present in tomato including both well-documented and completely new viruses. Some newly-emerged viruses in tomato were found to spread fast and therefore prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome we developed provides valuable information to facilitate the management of tomato viral diseases.