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      Identification of a TuMV isolate (TuMV-ZR) from Pseudostellaria heterophylla and its development into a viral expression vector

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          Highlights

          • A procedure to identify the viral genome was developed with virus-derived sRNAs.

          • P. heterophylla TuMV-ZR isolate (TuMV-ZR) were identified.

          • TuMV-ZR infectious clone effectively infected the medicinal plant P. heterophylla.

          • TuMV-ZR-based vectors continuously expressed foreign genes in P. heterophylla.

          Abstract

          Pseudostellaria heterophylla ( P. heterophylla) is a popular Chinese medicinal herb that is cultivated widely in China. Viral infection is commonly encountered during the production of P. heterophylla. To identify viruses causing P. heterophylla disease, sRNA and mRNA libraries were built for 2 sets of P. heterophylla plants, one set that was planted only once (FGP) and one that was planted three consecutive three times (TGP) in a field, using virus-free tuberous roots as reproductive materials. A comprehensive procedure, including assembling virus-derived sRNA (vsRNA), assessing and cloning the full-length viral genome, building an infectious cloning vector and constructing a virus-based expression vector, was performed to identify viruses infecting P. heterophylla. Ultimately, 48 contig-related viruses were mined from 6 sRNA and 6 mRNA P. heterophylla libraries. A 9762-bp fragment was predicted to be the complete genome of TuMV virus. This sequence was cloned from P. heterophylla, and its infectivity was evaluated using the virus-infection model plant Nicotiana benthamiana ( N. benthamiana) and host plant P. heterophylla. The resulting 9839-bp viral genome was successfully obtained from P. heterophylla and identified as a new P. heterophylla TuMV-ZR isolate. Simultaneously, TuMV-ZR infectious clones were shown to effectively infect P. heterophylla. Furthermore, TuMV-ZR expression vectors were developed, and the ability of a TuMV-ZR-based vector to express foreign genes was determined by analysis with the reporter gene EGFP. TuMV-ZR-based vectors were found to continuously express foreign genes in different organs of P. heterophylla throughout the whole vegetative period. In addition, TuMV-ZR vectors carrying EGFP accumulated in the tuberous roots of P. heterophylla, confirming that tuberous roots are key targets for viral infection and transmission. This study revealed the core pathogenicity of P. heterophylla mosaic virus and developed a new TuMV-ZR-based expression tool that led to long-term protein expression in P. heterophylla, laying the foundation for the identification of the mechanisms of P. heterophylla infection with mosaic viruses and developing tools to express value proteins in the tuberous roots of the medicinal plant P. heterophylla.

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          Most cited references47

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          Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

          We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
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            RNA virus interference via CRISPR/Cas13a system in plants

            Background CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. Results CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. Conclusions Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1381-1) contains supplementary material, which is available to authorized users.
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              Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses.

              We report the first identification of novel viruses, and sequence of an entire viral genome, by a single step of high-throughput parallel sequencing of small RNAs from diseased, as well as symptomless plants. Contigs were assembled from sequenced total siRNA from plants using small sequence assembly software and could positively identify RNA, ssDNA and dsDNA reverse transcribing viruses and in one case spanned the entire genome. The results present a novel approach which cannot only identify known viral pathogens, occurring at extremely low titers, but also novel viruses, without the necessity of any prior knowledge.
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                Author and article information

                Contributors
                Journal
                Virus Res
                Virus Res
                Virus Research
                Elsevier
                0168-1702
                1872-7492
                17 May 2023
                15 July 2023
                17 May 2023
                : 332
                : 199127
                Affiliations
                [a ]College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
                [b ]Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fuzhou 350002, China
                [c ]National Resource Center for Chinese Meteria Medica, State Key Laboratory of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
                [d ]Pharmaceutical Development Board of Zherong County, Ningde 352000, China
                Author notes
                [1]

                These authors contributed equally to this work.

                Article
                S0168-1702(23)00089-8 199127
                10.1016/j.virusres.2023.199127
                10345741
                37149225
                9dc0ae14-be10-4bd3-9509-99456921cb2e
                © 2023 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 10 February 2023
                : 30 April 2023
                : 3 May 2023
                Categories
                Article

                Microbiology & Virology
                pseudostellaria heterophylla,infectious clone,tumv-zr,virus-based expression vector,foreign proteins

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