*2.2. Phylogenetic Analysis*

A phylogenetic analysis based on 73 sequences recovered from species in the Trentepohliales consisted of two main clades. One main clade was composed of several small clades including the *Cephaleuros* clade, *T. aurea* clade, *T. arborum*, and *Printzina lagenifera* clade. The other main clade was composed by *Phycopeltis*, *Printzina bosseae*, *T. umbrina*, *T. iolithus*, and *T. annulata* (Figure S1). According to the 18S rDNA phylogeny, *T. odorata* had the closest relationship with *T. annulata* (KM020077) and *T.* cf. *umbrina* (KX586916) (Figure 2). According to the phylogeny based upon *rbc*L matrix, *T. odorata* clustered with Trentepohliales sp. (GU549443) and formed a robust clade with *T. annulata* (MH940266) and *T. abietina* (MH940276) (Figure 3). Such topology was consistent with previous studies. All of the analyses recovered *T. odorata* as a well resolved lineage.

**Figure 2.** The maximum likelihood phylogram inferred from 18S rDNA sequences of Trentepohliales. The monophyletic genus *Cephaleuros* was used as outgroup. Maximum likelihood bootstrap values (1000 replicates) and Bayesian posterior probabilities (PPs) are given near the nodes, and only bootstrap proportion (BP) and PP values above 50 and 0.50 are shown. The full statistical support (100/1.00) is marked with an asterisk. The *Trentepohlia odorata* was shaded in grey.

**Figure 3.** Maximum likelihood tree of Trentepohliales based on rbcL sequence data. Bayesian posterior probability (pp ≥ 0.50) and maximum likelihood (ML ≥ 50) bootstrap values are shown near the branches. The asterisks represent full statistical support (1.00/100). The *Trentepohlia odorata* was shaded in grey.

Our phylogenetic analysis based on chloroplast genome showed that both Trebouxiophyceae and Ulvophyceae were paraphyletic due to Chlorellaceae and the Bryopsidales, Trentepohliales, and Dasycladales clade (BDT clade) did not fall into core Trebouxiophyceae and core Ulvophyceae, respectively (Figure 4). Both maximum likelihood analysis and Bayesian analysis strongly supported that Trentepohliales clustered with Dasycladales. In the maximum likelihood analysis, the BDT clade was supported by a bootstrap value of 60; however, such topology did not occur in the Bayesian inference analysis (Figure S2). Both maximum likelihood analysis and Bayesian inference supported that Trentepohliales may have the closest relationship with Dasycladales.

**Figure 4.** Maximum likelihood tree inferred from a dataset consisted of 31 common cpDNA-encoded genes of 43 core Chlorophytes. The genera *Picocystis* (NC024828) and *Nephroselmis* (NC024829) were selected as outgroup. Maximum likelihood bootstrap values (1000 replicates) are given near the nodes. Taxonomic arrangement follows AlgaeBase, and *Trentepohlia odorata* is in red.
