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Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy
Zhu, Huan1; Hu, Yuxin1; Liu, Feng2; Hu, Zhengyu3; Liu, Guoxiang1
2019-04-01
Source PublicationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN1422-0067
Volume20Issue:7Pages:14
Abstract

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.

Keywordchloroplast genome free-standing ORFs introns phylogenetic analysis taxonomic study Trentepohlia odorata Trentepohliales
DOI10.3390/ijms20071774
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31600168] ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences[Y85Z061601]
WOS Research AreaBiochemistry & Molecular Biology ; Chemistry
WOS SubjectBiochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS IDWOS:000465258100079
WOS KeywordPRINTZINA TRENTEPOHLIALES ; SEQUENCE ALIGNMENT ; CATALYTIC INTRONS ; GREEN ; ANNOTATION ; ARCHITECTURE ; GENERATION ; DIVERSITY ; ALGORITHM ; HISTORY
PublisherMDPI
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences ; Featured Institute Service Project from the Institute of Hydrobiology, the Chinese Academy of Sciences
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/27627
Collection藻类生物学及应用研究中心
Corresponding AuthorLiu, Guoxiang
Affiliation1.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
Recommended Citation
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.
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