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Alignments of full and nearly full polyprotein-length nucleotide sequences from GenBank for the two ipomoviruses that cause cassava brown streak disease, in fasta format.  Separate alignments for 67 cassava brown streak virus sequences and 81 Ugandan cassava brown streak virus sequences are provided, as well as a combined alignment of 148 sequences.  Alignments were created with MUSCLE and then modified by eye in AliView. Also, two tree files (in nexus) format are supplied, resulting from a maximum likelihood analysis with IQTree on each of the two single-species datasets. Support for nodes with aLRT and 100 actual bootstrap replicates are provided (aLRT/bootstrap). 

The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa – which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10^3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 – 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.