**5. Conclusions**

The morphological observation and phylogenetic analysis recovered *Trentepohlia odorata* as a separate species. According to phylogenetic results, *Trentepohlia odorata* has the closest relationship with *Trentepohlia annulata*, which could be explained by the shared morphological evidence, i.e., the absent sporangiate-lateral. The chloroplast genome of *Trentepohlia odorata* is 399,372 bp, with 97 genes and 95 free-standing ORFs. The typical quadripartite structure of *Trentepohlia odorata* is different from Cladophorales and Bryopsidales. However, the fragmention of *rpo* gene clusters by in-frame stop codons and the frame shift mutation detected in the present study is similar to Bryopsidales. Our study describes the first chloroplast genome of Trentepohliales and provides new data for understanding the evolution of the chloroplast genome in BCDT clade. Since Trentepohliles is an exclusively aerial order in core Chlorophytes, future study focused on plastomes of the other Trentepohliaceaen groups such as *Trentepohlia aurea*, *Trentepohlia bosseae* and *Cephaleuros* might have more interesting findings.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/7/ 1774/s1. Figure S1. Maximum likelihood phylogram inferred from 18S rDNA sequences. Cladophorales was used as outgroup. Bootstrap values (1000 replicates) were given near the nodes. Figure S2. Bayesian tree inferred from a dataset consisted of 31 common cpDNA-encoded genes from 43 core Chlorophytes. Figure S3. The dot plot between the 21 contigs and one circular molecule.

**Author Contributions:** H.Z., G.L. and Z.H. conceived the study. H.Z., Y.H. and F.L. analyzed the data. H.Z. wrote the manuscript. All authors have read and approved the manuscript.

**Funding:** This research was funded by the National Natural Science Foundation of China (grant number 31600168) and the Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences (grant number Y85Z061601).

**Acknowledgments:** We are grateful to two anonymous reviewers, for their insightful and helpful comments and editorial corrections to improve our manuscript.

**Conflicts of Interest:** The authors declare that they have no competing interest.
