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Phylogenetic reconstruction using all publicly available ASFV whole-genome sequences.

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posted on 2020-08-27, 17:25 authored by Jan H. Forth, Leonie F. Forth, Sandra Blome, Dirk Höper, Martin Beer

The ML tree was constructed using IQ-TREE version 1.6.5 based on MAFFT version 7.388 aligned ASFV core-regions (approximately 137,000 bp from the 5′-A224 to the 3′-DP238L gene) downloaded from INSDC (status 13.05.2020). Standard model selection was used, resulting in the best-fit model GTR+F+R4 (general time reversible model with unequal rates and unequal base frequency + empirical base frequencies + FreeRate model with 4 categories). Statistical support of 10,000 ultrafast bootstraps using the ultrafast bootstrap approximation (UFBoot) (percentage values) is indicated at the nodes. Taxon names include, where available, ASFV designation and INSDC accession number and P72 GT. The scale bar represents number of substitutions per site. The update of the ASFV Georgia 2007/1 sequence from FR682468.1 to FR682468.2 is currently in progress, and FR682468.2 will be available from INSDC soon. The accession LR743116.1, wrongly assigned to the updated ASFV Georgia 2007/1 sequence, was removed from the databases. ASFV, African swine fever virus; GT, genotype; INSDC, International Nucleotide Sequence Database Collaboration; ML, maximum likelihood.