*3.8. Phylogenetic Analysis*

To determine the phylogenetic position of *P. granatum*, phylogenetic analysis was performed using the complete cp genomes in the Myrtales. The cp genomes previously published in the Myrtales and two species from Vitales were downloaded from NCBI using an in-house python script. Multiple sequences alignment was achieved by HomBlocks pipelines [73]. Some poorly aligned regions were removed with Gblocks [74]. Two methods were employed to construct a phylogenetic tree, including Maximum likelihood (ML), and Bayes inference (BI). The dataset was unpartitioned. ML was implemented in IQ-tree [69] under the best-fit model selected by using ModelFinder [75] according to Akaike information criterion (AIC). The ML tree was inferred with 1000 bootstrap replicates (the '-bb' options). BI was performed with MrBayes [76] under the best-fit model determined by Modeltest with the AIC. The Marjkov chain Monte Carlo (MCMC) analysis was run for 2 × 200,000 generations. Trees were sampled at every 1,000 generations with the first 25% discarded as burn-in. The stationarity was considered to be reached when the average standard deviation of split frequencies remained below 0.001. Phylogenetic trees with bootstrap values (BS) and posterior probabilities (PP) were visualized using R package 'ggtree' [77].
