Commentary: Plant Auxin Biosynthesis Did Not Originate in Charophytes

A commentary on Plant auxin biosynthesis did not originate in charophytes The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) family of aminotransferases and the YUCCA (YUC) family of flavin monooxygenases are required for the biosynthesis of auxin (Mashiguchi et al., 2011). However, the origin of TAA-YUC auxin biosynthesis pathway is under hot debate recently (Wang et al., 2014; Yue et al., 2014; Turnaev et al., 2015). By similarity searches and phylogenetic analyses, Yue et al. did not find TAA and YUC homologs in any algal group (Yue et al., 2014). On the contrary, we found TAA and YUC protein homologs in the genome of Klebsormidium flaccidum, a charophyte alga, and proposed that plant auxin biosynthesis might originate in charophytes (Wang et al., 2014). More recently, Turnaev et al. (2015) reanalyzed the structures and phylogenetic relationship of TAA family proteins and claimed K. flaccidum TAA-like protein (kfl00051_0080) is more closely related to alliinases than tryptophan aminotransferases. However, we believe this represents a common misinterpretation of phylogenetic tree, which leads to erroneous inferences of ancestry and evolutionary relationship. First, Turnaev et al. missed several TAA protein homologs in Choanoflagellida. We employed the BLASTP algorithm with Arabidopsis thaliana TAA1 protein as the query and found significant When the identity of protein pairs is higher than 25%, and the number of residues aligned is higher than 150, evolutionary relatedness could be convincingly inferred (Chung and Subbiah, 1996; Rost, 1999). It appears that these additional eukaryotic and prokaryotic proteins are homologous to A. thaliana TAA1 protein. Missing bacteria and archaea homologs leads to the absence of outgroup taxa to root the TAA phylogenetic tree (Figure 1A). Also, one key node (the clade of land plant alliinases, kfl00051_0080, and the Capsaspora owczarzaki sequence) is weakly supported (posterior probability: 0.463), making the deep relationship of plant and non-plant eukaryote TAA proteins unresolved. However, our phylogenetic tree with more non-plant eukaryote and prokaryote TAA-like proteins is more strongly supported in terms of posterior probability (see Figure 1D in this paper and Figure 1A in Wang et al., 2014). Most importantly, what Turnaev et al. present is an unrooted phylogenetic tree. Based on the unrooted phylogenetic tree, they claimed the kfl00051_0080 from K. flaccidum belongs to the land plant alliinase clade. Unfortunately, this claim results from a misinterpretation of phylogenetic