Journal: Molecular Plant-Microbe Interactions®

Article Title: Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

doi: 10.1094/mpmi-12-17-0301-r

Figure Lengend Snippet: Figure 1. Illumina sequencing counts of endogenous and viral sRNAs in S. tuberosum. The 20-25 nt sRNA libraries from healthy (BPO-148-149) and PVY+PVX (BPO-150-152) or PVY-AN+PVY-BO (BPO-147) virome-

Article Snippet: 722 Illumina sequencing and bioinformatics analysis of sRNAs 723 The 19-30 nt fractions of total RNA samples were sequenced at Fasteris 724 (www.fasteris.com) using TruSeq® small RNA Library Prep Kit (Illumina) for cDNA 725 library preparation, and multiplexing the potato (BPO-147-152) and tomato (BPO-156-726 165) libraries in separate lanes of the Genome Analyser HiSeq2500 or HiSeq 4000 727 (HYT-25-26).

Techniques: Illumina Sequencing

Journal: Molecular Plant-Microbe Interactions®

Article Title: Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

doi: 10.1094/mpmi-12-17-0301-r

Figure Lengend Snippet: Figure 2. Single-nucleotide resolution maps of viral sRNAs from leaf tissues of three plants grown from a potato tuber infected with a PVY-PVX virome. For each plant sample (BPO-150, BPO -151 and BPO -152),

Article Snippet: 722 Illumina sequencing and bioinformatics analysis of sRNAs 723 The 19-30 nt fractions of total RNA samples were sequenced at Fasteris 724 (www.fasteris.com) using TruSeq® small RNA Library Prep Kit (Illumina) for cDNA 725 library preparation, and multiplexing the potato (BPO-147-152) and tomato (BPO-156-726 165) libraries in separate lanes of the Genome Analyser HiSeq2500 or HiSeq 4000 727 (HYT-25-26).

Techniques: Infection

Journal: Molecular Plant-Microbe Interactions®

Article Title: Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

doi: 10.1094/mpmi-12-17-0301-r

Figure Lengend Snippet: Figure 5. Illumina sequencing counts of endogenous and viral sRNAs in S. lycopersicum plants infected with one (CH2) or two (CH2+LP) strains of PepMV. The 20-25 nt sRNA libraries from two healthy (BPO-164-165), two CH2-preinfected (BPO-160-161 and BPO-162-163) and two LP-preinfected (BPO-156-157 and BPO-158-

Article Snippet: 722 Illumina sequencing and bioinformatics analysis of sRNAs 723 The 19-30 nt fractions of total RNA samples were sequenced at Fasteris 724 (www.fasteris.com) using TruSeq® small RNA Library Prep Kit (Illumina) for cDNA 725 library preparation, and multiplexing the potato (BPO-147-152) and tomato (BPO-156-726 165) libraries in separate lanes of the Genome Analyser HiSeq2500 or HiSeq 4000 727 (HYT-25-26).

Techniques: Illumina Sequencing, Infection

Journal: Molecular Plant-Microbe Interactions®

Article Title: Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

doi: 10.1094/mpmi-12-17-0301-r

Figure Lengend Snippet: Figure 6. Single-nucleotide resolution maps of viral sRNAs from two tomato plants pre-infected with PepMV-

Article Snippet: 722 Illumina sequencing and bioinformatics analysis of sRNAs 723 The 19-30 nt fractions of total RNA samples were sequenced at Fasteris 724 (www.fasteris.com) using TruSeq® small RNA Library Prep Kit (Illumina) for cDNA 725 library preparation, and multiplexing the potato (BPO-147-152) and tomato (BPO-156-726 165) libraries in separate lanes of the Genome Analyser HiSeq2500 or HiSeq 4000 727 (HYT-25-26).

Techniques: Infection

Journal: Molecular Plant-Microbe Interactions®

Article Title: Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

doi: 10.1094/mpmi-12-17-0301-r

Figure Lengend Snippet: Figure 7. Single-nucleotide resolution maps of viral sRNAs from two tomato plants pre-infected with PepMV-

Article Snippet: 722 Illumina sequencing and bioinformatics analysis of sRNAs 723 The 19-30 nt fractions of total RNA samples were sequenced at Fasteris 724 (www.fasteris.com) using TruSeq® small RNA Library Prep Kit (Illumina) for cDNA 725 library preparation, and multiplexing the potato (BPO-147-152) and tomato (BPO-156-726 165) libraries in separate lanes of the Genome Analyser HiSeq2500 or HiSeq 4000 727 (HYT-25-26).

Techniques: Infection

Journal: Molecular Plant-Microbe Interactions®

Article Title: Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants

doi: 10.1094/mpmi-12-17-0301-r

Figure Lengend Snippet: Figure 8. Single-nucleotide resolution maps of contaminant Southern tomato virus (STV)-derived sRNAs from two tomato plants pre-infected with PepMV-CH2 and challenge-inoculated with PepMV-LP. For each plant sample at the two time points, 1.5 mpi (BPO-160 and BPO-162) and 6.5 mpi (BPO-161 and BPO-163),

Article Snippet: 722 Illumina sequencing and bioinformatics analysis of sRNAs 723 The 19-30 nt fractions of total RNA samples were sequenced at Fasteris 724 (www.fasteris.com) using TruSeq® small RNA Library Prep Kit (Illumina) for cDNA 725 library preparation, and multiplexing the potato (BPO-147-152) and tomato (BPO-156-726 165) libraries in separate lanes of the Genome Analyser HiSeq2500 or HiSeq 4000 727 (HYT-25-26).

Techniques: Virus, Derivative Assay, Infection

Journal: PLoS ONE

Article Title: Effects of Introduced and Indigenous Viruses on Native Plants: Exploring Their Disease Causing Potential at the Agro-Ecological Interface

doi: 10.1371/journal.pone.0091224

Figure Lengend Snippet: Introduced and indigenous viruses used: classifications, modes of transmission, host specificities and isolates.

Article Snippet: Pea seed-borne mosaic virus (PSbMV) , W1 , Vicia faba cv. Fiord (faba bean) , PSbMV , DSMZ.

Techniques: Transmission Assay, Virus

Journal: PLoS ONE

Article Title: Effects of Introduced and Indigenous Viruses on Native Plants: Exploring Their Disease Causing Potential at the Agro-Ecological Interface

doi: 10.1371/journal.pone.0091224

Figure Lengend Snippet: Introduced and indigenous viruses used: culture hosts for each isolate and antibodies for detection.

Article Snippet: Pea seed-borne mosaic virus (PSbMV) , W1 , Vicia faba cv. Fiord (faba bean) , PSbMV , DSMZ.

Techniques: Virus

Journal: PLoS ONE

Article Title: Effects of Introduced and Indigenous Viruses on Native Plants: Exploring Their Disease Causing Potential at the Agro-Ecological Interface

doi: 10.1371/journal.pone.0091224

Figure Lengend Snippet: Establishment of systemic or localised infection, or failure to establish infection, in 15 native plant species inoculated with introduced and indigenous viruses.

Article Snippet: Pea seed-borne mosaic virus (PSbMV) , W1 , Vicia faba cv. Fiord (faba bean) , PSbMV , DSMZ.

Techniques: Infection

Journal: Journal of Virology

Article Title: Variations in Hypovirus Interactions with the Fungal-Host RNA-Silencing Antiviral-Defense Response

doi: 10.1128/JVI.00961-12

Figure Lengend Snippet: Colony morphologies of wild-type Cryphonectria parasitica strain EP155 (left column) and mutant strain Δdcl2 (right column) following infection by hypoviruses CHV-1/EP713, CHV-1/Euro7, and CHV-1/EP721. The colony morphologies for the uninfected EP155 and Δdcl2 strains are shown at the top. Infections were initiated by transfection with the transcripts of the corresponding hypoviruses (3), and infected colonies were transferred to potato dextrose agar. The photographs were taken on day 7 of the experiment.

Article Snippet: The origins and sources of wild-type C. parasitica strain EP155 (ATCC 38755), the isogenic hypovirus CHV-1/EP713-containing strain EP713 (ATCC 52571), and CHV-1/Euro7-containing strain Euro7 (ATCC 66021) have been described by Chen and Nuss ( 5 ).

Techniques: Mutagenesis, Infection, Transfection

Journal: Journal of Virology

Article Title: Variations in Hypovirus Interactions with the Fungal-Host RNA-Silencing Antiviral-Defense Response

doi: 10.1128/JVI.00961-12

Figure Lengend Snippet: Accumulation of dcl2 transcripts in response to different hypoviruses. The relative levels of dcl2 transcripts were measured by semiquantitative real-time RT-PCR for uninfected strain EP155 and strain EP155 infected by CHV-1/EP713, CHV-1/Euro7, CHV-1/EP721, their corresponding Δp29 mutants, and the chimeric CHV-1/EP713 and CHV-1EP721 viruses containing the swapped p29 coding domains 713/721p29 and 721/713p29, as indicated at the bottom. The values on the y axis were normalized to the dcl2 transcript level in uninfected strain EP155, set to a value of 1.

Article Snippet: The origins and sources of wild-type C. parasitica strain EP155 (ATCC 38755), the isogenic hypovirus CHV-1/EP713-containing strain EP713 (ATCC 52571), and CHV-1/Euro7-containing strain Euro7 (ATCC 66021) have been described by Chen and Nuss ( 5 ).

Techniques: Quantitative RT-PCR, Infection

Journal: Journal of Virology

Article Title: Variations in Hypovirus Interactions with the Fungal-Host RNA-Silencing Antiviral-Defense Response

doi: 10.1128/JVI.00961-12

Figure Lengend Snippet: Hypovirus RNA accumulation in the C. parasitica Δdcl2 mutant strain. (A). Gel analysis of RNA isolated from hypovirus-infected wild-type C. parasitica strain EP155 and the Δdcl2 mutant strain. Approximately 10 μg of total nucleic acids isolated from each infected strain was loaded and subjected to electrophoresis in 1% agarose gels set at 15 V overnight. Lane 1 contains 0.5 μg of the in vitro-synthesized 12,734-nt transcript from infectious CHV-1/EP713 cDNA clone pRFL4 (see Materials and Methods). Lane M contains DNA size markers. Lanes 2 through 7 contain nucleic acids from strain EP155 infected with CHV-1/EP713, the Δdcl2 mutant infected with CHV-1/EP713, EP155 infected with CHV-1/Euro7, the Δdcl2 mutant infected with CHV-1/Euro7, EP155 infected with CHV-1/EP721, and the Δdcl2 mutant infected with CHV-1EP721, respectively. The migration positions of genomic DNA (gDNA) and the viral double-stranded replicative-form RNA (dsRNA) and positive-sense single-stranded viral RNA (+ssRNA) are indicated on the right. The bands migrating near the 8- to 10-kb markers in lane 2 (CHV-1/EP713-infected strain EP155) are defective viral RNAs commonly observed in infected wild-type C. parasitica strains but not observed in the RNA-silencing mutant Δdcl2 strain (38). Note the significant increase in accumulation of viral positive-sense ssRNA. (B). Relative accumulation of positive-sense ssRNA hypovirus RNA in infected wild-type C. parasitica strain EP155 and Δdcl2 mutant strain determined by real-time RT-PCR. The values on the y axis were normalized to the viral RNA levels in the infected wild-type strain EP155. The relative levels of positive-sense ssRNA for CHV-1/EP713, CHV-1/Euro7, and CHV-1/EP721 increased 33-, 32-, and 16-fold in the Δdcl2 strain relative to the levels in strain EP155, respectively.

Article Snippet: The origins and sources of wild-type C. parasitica strain EP155 (ATCC 38755), the isogenic hypovirus CHV-1/EP713-containing strain EP713 (ATCC 52571), and CHV-1/Euro7-containing strain Euro7 (ATCC 66021) have been described by Chen and Nuss ( 5 ).

Techniques: Mutagenesis, Isolation, Infection, Electrophoresis, In Vitro, Synthesized, Migration, Quantitative RT-PCR

Journal: Journal of Virology

Article Title: Variations in Hypovirus Interactions with the Fungal-Host RNA-Silencing Antiviral-Defense Response

doi: 10.1128/JVI.00961-12

Figure Lengend Snippet: Colony morphologies conferred by CHV-1/EP713–CHV-1/EP721 chimeric viruses in wild-type strain EP155 and the Δdcl2 mutant strain. (A) Schematic diagrams of chimeric viruses. The genomes of CHV-1/EP713 and CHV-1/EP721 contain two open reading frames designated ORF A and ORF B, as indicated at the top. The coding regions of individual chimeric viruses derived from the CHV-1/EP713 genome are indicated as blue boxes, and the CHV-1/EP721 genome-derived coding regions are indicated as white boxes. The autocatalytic cleavage sites for p29 and p48 are indicated by asterisks. The 5′ and 3′ noncoding terminal regions are indicated as lines. (B) Colony morphologies conferred by CHV-1/EP713–CHV-1/EP721 chimeric viruses in wild-type strain EP155 (left column) and the Δdcl2 mutant strain (right column). Infections were initiated by transfection with transcripts of the corresponding chimeric virus (3), and infected colonies were transferred to potato dextrose agar. The photographs were taken on day 7 of the experiment.

Article Snippet: The origins and sources of wild-type C. parasitica strain EP155 (ATCC 38755), the isogenic hypovirus CHV-1/EP713-containing strain EP713 (ATCC 52571), and CHV-1/Euro7-containing strain Euro7 (ATCC 66021) have been described by Chen and Nuss ( 5 ).

Techniques: Mutagenesis, Derivative Assay, Transfection, Virus, Infection