Content area
Full Text
About the Authors:
Rugang Li
Affiliation: U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, South Carolina, United States of America
Shan Gao
Affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America
Alvaro G. Hernandez
Affiliation: W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
W. Patrick Wechter
Affiliation: U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, South Carolina, United States of America
Zhangjun Fei
* E-mail: [email protected] (KSL); [email protected] (ZF)
Affiliations Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America, USDA Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
Kai-Shu Ling
* E-mail: [email protected] (KSL); [email protected] (ZF)
Affiliation: U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, South Carolina, United States of America
Introduction
Tomato (Solanum lycopersicum) is the world’s second most economically important vegetable, after potato, with a total world production in 2009 approaching 153 million tons in 173 countries [1]. The leading tomato producing countries are China, the United States, Italy, and Spain. Although most of the tomatoes are field-grown, protected production systems have increased significantly, particularly in Europe and North America, where several emerging viral diseases have caused serious damages to tomato crops in recent years [2].
In the last decade, Pepino mosaic virus (PepMV), genus Potexvirus and family Alphaflexiviridae, has emerged as one of the most economically important viruses infecting greenhouse tomatoes worldwide [3]. Several distinct genotypes of PepMV have been identified, including EU, US1 and CH2 [4], [5], [6], [7]. In recent years, other emerging diseases that are caused by several pospiviroids have been identified in North America [8], [9], [10], [11], are causing great concern to greenhouse tomato growers. In addition, there is always a concern that other, currently uncharacterized viruses may also be involved in these disease outbreaks.
Timely and accurate detection of phytopathogens is a prerequisite in making effective disease management decisions. Most virus detection methods [e.g., enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), or microarray] depend on prior knowledge of antibody or sequence of the potential virus. Advancement in next generation sequencing (NGS) technologies has provided a powerful alternative for total pathogen characterization without a priori knowledge.
A metagenomic...