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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&nbsp;Metadata Resource (VMR #18, 2021-10-19,&nbsp;<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.&nbsp;We confirmed the identity of misannotated ORF&nbsp;products by performing a BLAST search.&nbsp;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).&nbsp;After an initial alignment inspection, exemplars with either severely truncated (i.e., length &lt; 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.&nbsp;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 &amp; 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).&nbsp;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:&nbsp;exemplars sampled in the Americas in orange and&nbsp;exemplars sampled in the &#39;Africa, Asia, Europe and Oceania&#39; (AAEO) region in blue.&nbsp;</p> <p>METADATA</p> <p>Metadata associated with each ICTV-approved species&nbsp;exemplar (n=445) &ndash; 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 &ndash; are included. Exemplars not incorporated into the other analyses&nbsp;are highlighted in red on the spreadsheet.</p> <p>&nbsp;</p>