Journal: Viruses

Article Title: Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia

doi: 10.3390/v14020365

Figure Lengend Snippet: Genome architectures of the viruses identified in this study. Abbreviations are as follows: PtAEV, Pterostylis alphaendornavirus; PtAV1, Pterostylis amalgavirus 1; PtAV2, Pterostylis amalgavirus 2; PtTV, Pterostylis totivirus; PtPV, Pterostylis polerovirus; RdRp, RNA-dependent RNA polymerase; NSm, non-structural protein, M segment; NSs, non-structural protein, S segment; N, nucleocapsid protein; CP, capsid protein; nt, nucleotide; aa, amino acid.

Article Snippet: The RNA was polyadenylated using E. coli poly(A) polymerase (New England Biolabs) and cleaned up with a Monarch ® RNA Cleanup Kit (10 µg, New England Biolabs). cDNA was synthesised from the polyadenylated RNA using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) as per the manufacturer’s instructions, except that the custom primer 5′-CCACGCGTATCGATGTCGAC(dT)40VN-3′ was used instead of the recommended oligo(dT)18 primer.

Techniques:

Journal: Viruses

Article Title: Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia

doi: 10.3390/v14020365

Figure Lengend Snippet: Maximum likelihood reconstruction of the phylogeny of orthotospoviruses based on concatenated sequence alignments of five genes (RNA-dependent RNA polymerase, non-structural protein M segment, glycoprotein precursor, non-structural protein S segment and nucleocapsid protein). The acronyms in red font correspond to the viruses discovered in this study and the other virus acronyms are defined in . The numbers to the left of the slash next to the branches are non-parametric bootstrap values based on 1000 replicates; the numbers to the right of the slash are the number of decisive gene trees (5 at maximum) supporting the branch. The nucleotide substitution models used are listed in .

Article Snippet: The RNA was polyadenylated using E. coli poly(A) polymerase (New England Biolabs) and cleaned up with a Monarch ® RNA Cleanup Kit (10 µg, New England Biolabs). cDNA was synthesised from the polyadenylated RNA using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) as per the manufacturer’s instructions, except that the custom primer 5′-CCACGCGTATCGATGTCGAC(dT)40VN-3′ was used instead of the recommended oligo(dT)18 primer.

Techniques: Sequencing

Journal: Viruses

Article Title: Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia

doi: 10.3390/v14020365

Figure Lengend Snippet: Maximum likelihood reconstruction of the phylogeny of alphaendornaviruses based on the RNA-dependent RNA polymerase gene. The acronym in red font corresponds to the virus discovered in this study and the other virus acronyms are defined in . The numbers next to the branches are non-parametric bootstrap values based on 1000 replicates. The nucleotide substitution model used for the phylogenetic tree is listed in .

Article Snippet: The RNA was polyadenylated using E. coli poly(A) polymerase (New England Biolabs) and cleaned up with a Monarch ® RNA Cleanup Kit (10 µg, New England Biolabs). cDNA was synthesised from the polyadenylated RNA using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) as per the manufacturer’s instructions, except that the custom primer 5′-CCACGCGTATCGATGTCGAC(dT)40VN-3′ was used instead of the recommended oligo(dT)18 primer.

Techniques:

Journal: Viruses

Article Title: Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia

doi: 10.3390/v14020365

Figure Lengend Snippet: Maximum likelihood reconstruction of the phylogeny of amalgaviruses based on the RNA dependent RNA polymerase gene. The acronyms in red font correspond to the viruses discovered in this study and the other virus acronyms are defined in . The numbers next to the branches are non-parametric bootstrap values based on 1000 replicates. The nucleotide substitution model used for the phylogenetic tree is listed in .

Article Snippet: The RNA was polyadenylated using E. coli poly(A) polymerase (New England Biolabs) and cleaned up with a Monarch ® RNA Cleanup Kit (10 µg, New England Biolabs). cDNA was synthesised from the polyadenylated RNA using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) as per the manufacturer’s instructions, except that the custom primer 5′-CCACGCGTATCGATGTCGAC(dT)40VN-3′ was used instead of the recommended oligo(dT)18 primer.

Techniques:

Journal: Viruses

Article Title: Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia

doi: 10.3390/v14020365

Figure Lengend Snippet: Maximum likelihood reconstruction of the phylogeny of totiviruses based on the RNA-dependent RNA polymerase gene. The acronyms in red font correspond to the viruses s discovered in this study and the other virus acronyms are defined in . The numbers next to the branches are non-parametric bootstrap values based on 1000 replicates. The nucleotide substitution model used for the phylogenetic tree is listed in .

Article Snippet: The RNA was polyadenylated using E. coli poly(A) polymerase (New England Biolabs) and cleaned up with a Monarch ® RNA Cleanup Kit (10 µg, New England Biolabs). cDNA was synthesised from the polyadenylated RNA using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) as per the manufacturer’s instructions, except that the custom primer 5′-CCACGCGTATCGATGTCGAC(dT)40VN-3′ was used instead of the recommended oligo(dT)18 primer.

Techniques:

Journal: Viruses

Article Title: Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia

doi: 10.3390/v14020365

Figure Lengend Snippet: Maximum likelihood reconstruction of the phylogeny of poleroviruses based on concatenated codon sequence alignments of the conserved regions of four genes (serine proteinase, RNA-dependent RNA polymerase, capsid protein (P3) and the domain at the C-terminus of P3 in P3–P5 readthrough protein). The acronym in red font corresponds to the virus isolate discovered in this study and the other virus acronyms are defined in . The numbers to the left of the slash next to the branches are non-parametric bootstrap values based on 1000 replicates; the numbers to the right of the slash are the number of decisive gene trees (4 at maximum) supporting the branch. The nucleotide substitution models are listed in .

Article Snippet: The RNA was polyadenylated using E. coli poly(A) polymerase (New England Biolabs) and cleaned up with a Monarch ® RNA Cleanup Kit (10 µg, New England Biolabs). cDNA was synthesised from the polyadenylated RNA using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) as per the manufacturer’s instructions, except that the custom primer 5′-CCACGCGTATCGATGTCGAC(dT)40VN-3′ was used instead of the recommended oligo(dT)18 primer.

Techniques: Sequencing