*2.3. Phylogenetic Analysis and Conserved Motifs*

We generated a phylogenetic tree to investigate the evolutionary connections of the water lily *SOD* gene family. This was done using protein sequences from *N. colorata*, *N. mexicana*, *N. minuta*, *N. thermarum*, and *A. trichopoda* (*Amborella trichopoda*). First, we aligned the protein sequences using MUSCLE with default parameters [39]. Then, we used the MEGA11 software (https://megasoftware.net/home accessed on 27 January 2023) to make a phylogenetic tree using the Neighbor-Joining algorithms. We assigned confidence levels to each branch of the tree using bootstrap tests (1000). We used the MEME server (https://meme-suite.org/meme/db/motifs accessed on 2 February 2023) with default settings to detect conserved motifs in the protein sequences of water lily *SODs* [40].
