Multiplex RT-PCR to simultaneously detect three viruses that infect peach

Purification of Total RNAs and Small RNAs from Fruit Tree Leaf Tissues

Perennial fruit crops are susceptible to many viral pathogens, which often lead to declines in quality and yield. For the production of good quality and virus-free propagation materials, conventional molecular detection methods combining high throughput sequencing technology have been widely applied to virus detection and discovery in fruit trees. Recovery of high-quality RNAs from fruit tree leaf tissues, the critical step for the subsequent molecular analysis, is often complicated by the presence of high levels of RNases and problematic biomolecules. Therefore, the universal extraction methods often require modification according to different properties of various tissues. In this chapter, we provide a set of methods that have been used successfully to isolate total RNAs and small RNAs from various fruit tree leaf tissues and as examples, presented in detail of a modified TRIzol method for total RNAs purification from mulberry (Morus alba L.) leaf tissues and an alternative small RNAs purification protocol using mirVana™ miRNA isolation kit (Ambion/Life Technologies) for some fruit tree leaf tissues. The protocols described here aim to provide examples of what have worked successfully for a range of fruit trees and may be successful for a given sample in the future.

Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.