New Experimental Hosts of Tobacco streak virus and Absence of True Seed Transmission in Leguminous Hosts

Development of full-length infectious cDNA clones and host range identification of an echinacea strain of tobacco streak virus

Tobacco streak virus induces severe diseases on a wide range of plants and becomes an emerging threat to crop yields. However, the infectious clones of TSV remain to be developed for reverse genetics studies. Here, we obtained the full genome sequence of a TSV-CNB isolate and analyzed the phylogenetic characteristics. Subsequently, we developed the full-length infectious cDNA clones of TSV-CNB driven by 35 S promoter using yeast homologous recombination. Furthermore, the host range of TSV-CNB isolate was determined by Agrobacterium infiltration and mechanical inoculation. The results reveal that TSV-CNB can infect 10 plant species in 5 families including Glycine max, Vigna radiate, Lactuca sativa var. Ramosa, Dahlia pinnate, E. purpurea, Calendula officinalis, Helianthus annuus, Nicotiana. Benthamiana, Nicotiana tabacum and Chenopodium quinoa. Taken together, the TSV infectious clones will be a useful tool for future studies on viral pathogenesis and host-virus interactions.

Detection and discovery of plant viruses in soybean by metagenomic sequencing

BACKGROUND

Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available.

METHODS

In this study, soybean fields were scouted for virus-like disease symptoms during the 2016-2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes.

RESULTS

Several viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common.

CONCLUSIONS

Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.

Complete genome sequence and phylogenetic relationships of tobacco streak virus causing groundnut stem necrosis disease in India

Tobacco streak virus (TSV, genus Ilarvirus family Bromoviridae) is known to cause stem necrosis disease (SND) in groundnut (Arachis hypogaea) since 2000 in Southern India. The TSV isolate infecting groundnut so far has not been characterized based on the complete genome sequence. In this study, TSV was isolated from a naturally infecting groundnut plant in Kadiri, the hot-spot of the SND in southern India. During the Kharif season of 2014, groundnut plants in an experimental field were affected with chlorosis and necrosis in leaf, stem and buds. The cent percent of the 48 samples with these symptoms collected from the field tested positive for TSV in ELISA samples in this context. One isolate, GN-Kad was established from a single lesion on cowpea cv. C-152 through successive sap inoculation. Cloning and sequencing of coat protein gene (717 nucleotides) of the isolate showed high sequence identity (98-99%) with the TSV isolates reported from different crops in India. The isolate produced local necrotic rings or veinal necrosis following sap inoculation to cowpea (cultivars C-152, Pusa Komal, Pusa Sukomal and Krishi Kanchan), French bean and sunflower; whereas, it produced systemic chlorotic mottling symptoms in Nicotiana benthamiana. The three segments of the virus genome (RNA 1, RNA 2 and RNA 3) contained 3523, 2903 and 2232 nucleotides, respectively. The overall genome sequence (8639 nt) of the present isolate shared 77-99% of nucleotide sequence identity with that of the other seven isolates reported from Australia, India and USA. The GN-Kad shared very close phylogenetic relationship with the okra and pumpkin isolates reported from India. The present report is the first comprehensive study of the molecular characterization of TSV associated with the stem necrosis disease of groundnut.

Complete nucleotide sequences and construction of full-length infectious cDNA clones of cucumber green mottle mosaic virus (CGMMV) in a versatile newly developed binary vector including both 35S and T7 promoters

Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome. Three CGMMV isolates (OMpj, Wpj, and Mpj) were separately evaluated for infectivity in Nicotiana benthamiana, demonstrated by either Agroinfiltration or inoculation with in vitro RNA transcripts. CGMMV nucleotide identities to other tobamoviruses were calculated from pairwise alignments using DNAMAN. CGMMV identities were 49.89% to tobacco mosaic virus; 49.85% to pepper mild mottle virus; 50.47% to tomato mosaic virus; 60.9% to zucchini green mottle mosaic virus; and 60.96% to kyuri green mottle mosaic virus, confirming that CGMMV is a distinct species most similar to other cucurbit-infecting tobamoviruses. We further performed phylogenetic analysis to determine relationships of our new Korean CGMMV isolates to previously characterized isolates from Canada, China, India, Israel, Japan, Korea, Russia, Spain, and Taiwan available from NCBI. Analysis of CGMMV amino acid sequences showed three major clades, broadly typified as 'Russian,' 'Israeli,' and 'Asian' groups. All of our new Korean isolates fell within the 'Asian' clade. Neither the 128 nor 186 kDa RdRps of the three new isolates showed any detectable gene silencing suppressor function.

Comparative reaction of popular high yielding spanish and virginia bunch groundnut varieties to Tobacco streak virus

Reaction of five spanish (JL 24, TMV 2, Kadiri 6, Kadiri 9 and Anantha) and a virginia (Kadiri 7 Bold) groundnut cultivars was studied against Tobacco streak virus (TSV) by sap inoculation using different age group of plants [7-84 days after sowing (DAS)]. Among different cultivars, incubation period varied from 4 to 28 days and high incubation period recorded in Kadiri 7 Bold. The percent infection decreased with increase in the age of the plants in all the cultivars as it ranged up to 100 % in both pre-flowering (7-21 DAS) and flowering stage (28-63 DAS) plants followed by 50-100 % in maturity stage plants (70-84 DAS) except Kadiri 7 Bold. Similarly, 100 % wilting was observed in pre flowering stage plants against no wilting in maturity stage plants. However, cultivars differed in per cent wilting of flowering stage plants by recording maximum wilting (100 %) in JL24, Kadiri 6 and minimum (25.0 %) in Kadiri 7 Bold. Both localized (necrotic spots, veinal necrosis) and systemic (petiole necrosis, necrotic spots on young leaves, top growing bud and stem necrosis, axillary shoot proliferation, stunting, peg necrosis, pod necrosis, wilting of plant) symptoms induced by TSV were similar among all cultivars without any new symptoms. Prolonged stage of axillary shoot proliferation was observed for the first time in all the cultivars. In maturity stage plants of Kadiri 7 Bold, Kadiri 9 and Anantha, systemic symptoms restricted to leaf and petiole necrosis only. Virus titer varied significantly with the age of plants and inoculum harvest at days post inoculation and least virus titer recorded by Kadiri 7 Bold at all stages of infection. Among different cultivars, Kadiri 7 Bold was least susceptible/tolerant to TSV by registering higher incubation period with less per cent infection, wilt and titer.