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

doi:10.3390/ijms20071774

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	Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy
	Zhu, Huan 1; Hu, Yuxin 1; Liu, Feng 2; Hu, Zhengyu 3; Liu, Guoxiang 1
刊名	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
	2019-04-01
卷号	20 期号:7 页码:14
关键词	chloroplast genome free-standing ORFs introns phylogenetic analysis taxonomic study Trentepohlia odorata Trentepohliales
ISSN号	1422-0067
DOI	10.3390/ijms20071774
通讯作者	Liu, Guoxiang(liugx@ihb.ac.cn)
英文摘要	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.
资助项目	National Natural Science Foundation of China[31600168] ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences[Y85Z061601]
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
语种	英语
出版者	MDPI
WOS记录号	WOS:000465258100079
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/161249]
专题	海洋研究所_海洋生态与环境科学重点实验室
通讯作者	Liu, Guoxiang
作者单位	1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Algal Biol, Wuhan 430072, Hubei, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Shandong, Peoples R China 3.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Hubei, Peoples R China
推荐引用方式 GB/T 7714	Zhu, Huan,Hu, Yuxin,Liu, Feng,et al. Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2019,20(7):14.
APA	Zhu, Huan,Hu, Yuxin,Liu, Feng,Hu, Zhengyu,&Liu, Guoxiang.(2019).Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,20(7),14.
MLA	Zhu, Huan,et al."Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 20.7(2019):14.