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8 results for “begomovirus”
Begomovirus DNA-B Movement Protein and Nuclear Shuttle Protein Ref-Seq Datasets
<p>Multiple Sequence Alignment of proteins encoded on begomovirus DNA-B (movement protein and nuclear shuttle protein; n=131). One isolate per species based on ICTV reference list.</p> <p> </p>
Coat protein (CP) and trimmed replication-associated protein (Rep) amino acid alignments, phylogenetic analyses, and associated metadata for ICTV-approved begomovirus RefSeq species exemplars
<p>DATA RETRIEVAL</p> <p>Annotated begomovirus coding sequences corresponding to each begomovirus species exemplar with a RefSeq accession number listed in the ICTV Virus Metadata Resource (VMR #18, 2021-10-19, <a href="https://ictv.global/vmr">https://ictv.global/vmr</a>) were downloaded from GenBank in protein FASTA file format. CP and Rep amino acid sequences were extracted and split into separate data sets for analysis. We confirmed the identity of misannotated ORF products by performing a BLAST search. For exemplar sequences missing ORF annotations (listed in metadata spreadsheet), ORFfinder (<a href="https://www.ncbi.nlm.nih.gov/orffinder/">https://www.ncbi.nlm.nih.gov/orffinder/</a>) was used to identify CP and Rep ORFs that were subsequently translated and added to each corresponding data set after BLAST confirmation.</p> <p>ALIGNMENTS</p> <p>Multiple sequence alignments were constructed using the MUSCLE method (Edgar, 2004) as implemented in MEGA 11 (Tamura et al., 2021) and manually corrected using AliView v1.26<strong> </strong>(Larsson, 2014). After an initial alignment inspection, exemplars with either severely truncated (i.e., length < 50% of the average length of the protein) or very divergent (i.e., causing us to doubt protein homology) CP or Rep sequences were excluded from the data set. Due to the difficulties in aligning the Rep sequences at the N- and C- terminal ends, the Rep alignment was trimmed to eliminate all residues prior to the iteron related domain (i.e., the known Rep functional region closest to the Rep start (Arguello-Astorga & Ruiz-Medrano, 2001)) in the N-terminus and after a conserved geminivirus motif found near the C-terminus, which corresponds to where other circular, Rep-encoding single-stranded DNA viruses possess an arginine finger motif (Kazlauskas et al., 2019; Krupovic et al., 2020). In total, our CP and Rep data sets contained amino acid sequences from 432 begomovirus species exemplars that met our inclusion criteria.</p> <p>PHYLOGENETIC ANALYSIS</p> <p>Maximum likelihood (ML) trees were inferred with IQ-Tree v2.0.7 (Minh et al., 2020) using the best fitting substitution model identified by the built-in ModelFinder feature (Kalyaanamoorthy et al., 2017). Tree inference was performed with 3000 ultrafast bootstrap (UFBoot) replicates, a perturbation strength of 0.2 and a stopping rule requiring an iteration interval of 500 iterations between unsuccessful improvements to the local optimum. The -bnni flag was enabled to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. The provided phylogenies in NEXUS format are midpoint-rooted and branches are colored based on traditional begomovirus geographic groupings: exemplars sampled in the Americas in orange and exemplars sampled in the 'Africa, Asia, Europe and Oceania' (AAEO) region in blue. </p> <p>METADATA</p> <p>Metadata associated with each ICTV-approved species exemplar (n=445) – including country of isolation, geographic designation (i.e., AAEO/Americas), genome segmentation (i.e., monopartite/bipartite), presence/absence of V2/AV2 gene and length of genome/DNA-A segments – are included. Exemplars not incorporated into the other analyses are highlighted in red on the spreadsheet.</p> <p> </p>
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 known complete genomes of AlYVV from databank and two complete genomes determined in this study (indicated in black boxes). The tree was rooted on ToLCNDV (AB613826) as an out-group. The schematic representation of recombination events detected by RDP4. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: pre-coat protein (AV2), coat protein (CP), replication-associated proteins (Rep and REn), transcriptional protein (TrAP), and AC4 region. AlYVV from different countries were colored differently. The colors of blocks represent the different ALYVV species and strains. Numbers at nodes indicate bootstrap confidence scores (1000 replicates).
Figure 1 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 1. Sonchus Palustris plant and cloning of begomovirus: (A) Asymptomatic plant showing vein yellowing symptoms; (B) Symptomatic plant; (C) Amplification using Phi29 DNA polymerase, restriction and cloning of viral molecules; (lane 1-2) Amplified RCA product, (lane 3-4) restriction of RCA product resulted in 2.8kb fragment usingEco RI, (lane 6-7) Confirmation of cloning of virus 2.8kb in pTZ57R vector using EcoRI and Hindlll, lane 5 shows 1Kb marker. Size of pTZ57R vector is also 2.88 Kb.
Figure 4 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 4. Comparison of the phylogenetic trees of the Rep-gene (A) and CP-gene (B) of AlYVV for recombination analysis. AlYVV from different countries were colored differently. Lines show assortment of Rep gene and CP genes in different clusters showing intraspecific recombination. Rep and CP gene from AlYVV determined in this study are indicated in black boxes. Clade I contains AlYVV and clade II encompasses closely related viruses like LuYVVNV, RaLCV and AEV. The trees were arbitrarily rooted on the sequences of the Tomato leaf curl New Delhi virus (AB613826). Numbers at nodes indicate bootstrap confidence scores (1000 replicates).
Figure 2 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 2. Color-coded matrix of pairwise nucleotide identity inferred from alignment of full-length AlYVV present in data bank. The matrix uses a discontinuous range of three shades of color (red, green and blue) differentiating two cut-off values representing the strain (93-94%, brown red) and the species (90-91%, yellow green) demarcation thresholds of begomoviruses. Identities were calculated with SDT v. 1.2.
A Crop Plant Integrates and Coordinates its Defenses to Cope with the Attack by Begomovirus and Whitefly
GEO Series GSE29812. Nicotiana tabacum. 4 samples. Type: Expression profiling by high throughput sequencing.
Constitutive activation of the receptor-like kinase NIK impairs translation and confers tolerance to begomovirus infection
GEO Series GSE38028. Solanum lycopersicum. 12 samples. Type: Expression profiling by high throughput sequencing.
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