HvAPX1 Phylogenetic Analysis

To assess the evolutionary relationship of HvAPX1, which has been described as a plant-like peroxidase, a comparative BLAST analysis was performed using ascorbate peroxidases from a range of organisms. HvAPX1 was compared with multiple plant ascorbate peroxidases from <i>Arabidopsis thaliana</i>, including the stromal ascorbate peroxidase (Q42592), the thylakoid-bound ascorbate peroxidase (Q42593) and the cytosolic L-ascorbate peroxidase 1 (Q05431), and L-ascorbate peroxidase 3 (Q42564), as well as the cytosolic ascorbate peroxidase from <i>Pisum sativum </i>(P48534). In addition, the L-ascorbate peroxidase from <i>Glycine max</i> (Q39843) was included. To place HvAPX1 in a broader symbiotic context, peroxidases from other symbiotic host organisms were also analysed, including those from <i>Euglena gracilis</i> (Q8LP26) and <i>Galdieria partita </i>(Q8GT26). Furthermore, the ascorbate peroxidase from the <i>Chlorella</i> symbiont (Q4QSD9) of <i>Hydra viridissima</i> was included, alongside the ascorbate peroxidase from <i>Chlorella sorokiniana</i> (A0A2P6TMU0) as a free-living reference species. Finally, mitochondrial cytochrome c peroxidases from <i>Leishmania major</i> and <i>Trypanosoma cruzi</i> were incorporated into the analysis. These comparisons follow approaches previously applied by Adak et al. (2005), et al. (2002), and Habetha et al. (2005) (Adak &amp; Datta, 2005; Habetha &amp; Bosch, 2005; Wilkinson et al., 2002). In addition, peroxidases from <i>Symbiodiniaceae</i> were included to further contextualise HvAPX1 within symbiotic systems of cnidaria.Evolutionary analysis by Maximum Likelihood method The evolutionary history was inferred by using the Maximum Likelihood method and Whelan And Goldman + Freq. model [1]. The tree with the highest log likelihood (-36460.11) is shown. 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 the JTT model, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1.3960)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 0.27% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. This analysis involved 63 amino acid sequences. There were a total of 1856 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [2]<br><br>1. Whelan, S. and Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution 18:691-699.2. Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35:1547-1549.3. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided "as is" without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (www.megasoftware.net). In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application.