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deep sequencing of small rnas in tomato for virus and viroid identification and strain differentiation深度测序的小rna病毒和类病毒识别番茄和应变分化
Deep Sequencing of Small RNAs in Tomato for Virus and Viroid Identification and Strain Differentiation 1 2 3 1 2,4 1 Rugang Li , Shan Gao , Alvaro G. Hernandez , W. Patrick Wechter , Zhangjun Fei *, Kai-Shu Ling * 1 U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, South Carolina, United States of America, 2 Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America, 3 W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, 4 USDA Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America Abstract Small RNAs (sRNA), including microRNAs (miRNA) and small interfering RNAs (siRNA), are produced abundantly in plants and animals and function in regulating gene expression or in defense against virus or viroid infection. Analysis of siRNA profiles upon virus infection in plant may allow for virus identification, strain differentiation, and de novo assembly of virus genomes. In the present study, four suspected virus-infected tomato samples collected in the U.S. and Mexico were used for sRNA library construction and deep sequencing. Each library generated between 5–7 million sRNA reads, of which more than 90% were from the tomato genome. Upon in-silico subtraction of the tomato sRNAs, the remaining highly enriched, virus-like siRNA pools were assembled with or without reference virus or viroid genomes. A complete genome was assembled for Potato spindle tuber viroid (PSTVd) using siRNA alone. In addition, a near complete virus genome (98%) also was assembled for Pepino mosaic virus (PepMV). A common mixed infection o
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