Figure 3
From: Auxin perception in Agave is dependent on the species’ Auxin Response Factors
Phylogenetic relationship of the ARF of Agave to other species. Phylogeny was calculated from an MSA of the 30 putative A. tequilana ARFs (marked by solid blue circles) plus 127 ARFs from seven previously reported plant species (15 ARF of Cucumis sativus54, 19 of Vitis vinifera55, 20 of Solanum lycopersicum56, 22 of A. thaliana57, 20 in Oryza sativa58, and 31 in Zea mays59). The evolutionary history was inferred using the Minimum Evolution method81. The optimal tree with the sum of branch length = 52.16578416 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method80 and are in the units of the number of amino acid substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1.011). The ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm83 at a search level of 2. The Neighbor-joining algorithm84 was used to generate the initial tree. The analysis involved 158 amino acid sequences. All ambiguous positions were removed for each sequence pair. There were a total of 1827 positions in the final dataset. Evolutionary analyses were conducted in MEGA785.
