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Figure 7 | BMC Genomics

Figure 7

From: The grapevine gene nomenclature system

Figure 7

Molecular phylogenetic analysis of Vitis vinifera trihydroxystilbene synthase gene models by the Maximum Likelihood method. Multiple sequence alignment for full-length trihydroxystilbene synthases was inferred using MUSCLE [36] from the nucleotide sequence. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [37]. The bootstrap consensus tree inferred from 100 replicates [38] is taken to represent the evolutionary history of the taxa analyzed [38]. Branches corresponding to partitions reproduced in less than 70% of bootstrap replicates were collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) is shown next to the branches [38]. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The analysis involved 40 amino acid sequences. The coding data was translated assuming a standard genetic code table. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 292 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [39]. Arrows point toward recommended Vitis symbols. A,B,C refer to the groups in [4].

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