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. 2014 Apr 15;15(8):790–801. doi: 10.1111/mpp.12137

Figure 5.

figure

 Phylogenetic neighbour‐joining tree built from the nucleotide sequences of badnavirus RT‐RNaseH domain amplified from Dioscorea rotundata seedlings Sd1 and Sd2. Primer sequences were removed. Bootstrap values of 1000 replicates are given above the nodes when above 80% (Tamura et al., 2004) and the evolutionary distances were computed using the HKY model. The first letter and number of the sequences refer to the seedling names, with S1 referring to Sd1 and S2 to Sd2. G1Dr (underlined), sequence of the RT‐RNaseH domain of the rearranged sequence G1Dr (fragment 19; see Fig. 1A) and sequence ‘1.13’ from a strain of DBALV, which was used as a probe in Southern blot experiments, are included. Additional sequences of the badnavirus RT/RNaseH domain were used: Dioscorea bacilliform alata virus (DBALV) and Dioscorea bacilliform sansibarensis virus (DBSNV) sequences and previously reported sequences from yam badnaviruses. Banana streak Goldfinger virus (BSGFV) and Taro bacilliform virus (TABV), used as members of the genus Badnavirus, and Cauliflower mosaic virus (CaMV) and Rice tungro bacilliform virus (RTBV), used as outgroups, are also shown. The scale bar shows the number of substitutions per base.