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Article

Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy

1
Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
2
Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
3
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(7), 1774; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071774
Received: 8 March 2019 / Revised: 8 April 2019 / Accepted: 8 April 2019 / Published: 10 April 2019
(This article belongs to the Special Issue Organelle Genetics in Plants)
Trentepohliales is an aerial order of Chlorophyta with approximately 80 species distributed mainly in tropical and subtropical regions. The taxonomy of this genus is quite difficult and presents a challenge for many phycologists. Although plentiful molecular data is available, most of the sequences are not identified at the species level. In the present study, we described a new specimen with detailed morphological data and identified it as Trentepohlia odorata. A phylogenetic analysis showed T. odorata as a novel lineage in Trentepohliales. T. odorata has the closest relationship with T. annulata, which is expected since sporangia of both species are without stalk cell and with dorsal pore. Species with such morphological characteristics may represent deep lineages in Trentepohliales. Although an increasing number of chloroplast genomes of Ulvophyceae have been reported in recent years, the whole plastome of Trentepohliales has not yet been reported. Thus, the chloroplast genome of Trentepohlia odorata was reported in the present study. The whole plastome was 399,372 bp in length, with 63 predicted protein-coding genes, 31 tRNAs, and 3 rRNAs. Additionally, we annotated 95 free-standing open reading frames, of which seven were annotated with plastid origins, 16 with eukaryotic genome origins, and 33 with bacterial genome origins. Four rpo genes (rpoA, rpoB, rpoC1, and rpoC2) were annotated within ORF clusters. These four genes were fragmented into several (partial) ORFs by in-frame stop codons. Additionally, we detected a frame shift mutation in the rpoB gene. The phylogenetic analysis supported that Trentepohliales clustered with Dasycladales and nested into the BDT clade (Bryopsidales, Dasycladales and Trentepohliales). Our results present the first whole chloroplast genome of a species of Trentepohliales and provided new data for understanding the evolution of the chloroplast genome in Ulvophyceae. View Full-Text
Keywords: chloroplast genome; free-standing ORFs; introns; phylogenetic analysis; taxonomic study; Trentepohlia odorata; Trentepohliales chloroplast genome; free-standing ORFs; introns; phylogenetic analysis; taxonomic study; Trentepohlia odorata; Trentepohliales
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MDPI and ACS Style

Zhu, H.; Hu, Y.; Liu, F.; Hu, Z.; Liu, G. Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy. Int. J. Mol. Sci. 2019, 20, 1774. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071774

AMA Style

Zhu H, Hu Y, Liu F, Hu Z, Liu G. Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy. International Journal of Molecular Sciences. 2019; 20(7):1774. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071774

Chicago/Turabian Style

Zhu, Huan, Yuxin Hu, Feng Liu, Zhengyu Hu, and Guoxiang Liu. 2019. "Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy" International Journal of Molecular Sciences 20, no. 7: 1774. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071774

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