Skip to main content
SpringerLink
Log in

The complete chloroplast genome of the green algae Hariotina reticulata (Scenedesmaceae, Sphaeropleales, Chlorophyta)

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

In this study, the chloroplast genome of Hariotina reticulata was fully sequenced and compared to other Sphaeropleales chloroplast genomes. It is 210,757 bp larger than most Sphaeropleales cpDNAs. It presents a traditional chloroplast structure, and contains 103 genes, including 68 protein-coding genes, six rRNA genes and 29 tRNA genes. The coding region constitutes of 43% of the whole cpDNA. Eighteen introns are found in 11 genes and six introns are unique for Hariotina. 11 open reading frames are identified among these introns. The synteny between Hariotina and Acutodesmus cpDNAs is in general identical, while within Sphaeropleales order, high variability in cpDNA architecture is indicated by general high DCJ distances. Ankyra judayi exhibits the greatest dissimilarity in gene synteny to the others and share some unique gene clusters with Treubaria triappendiculata. The phylogenomic analyses show that A. judayi is clustered with Treubariaceae species and sister to Chlorophyceae incertae sedis and other Sphaeropleales species. The monophyly of Sphaeropleales is rejected.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H et al (2011) tRNADB-CE 2011: tRNA gene database curated manually by experts. Nucleic Acids Res 39:210–213. https://doi.org/10.1093/nar/gkq1007

    Article  Google Scholar 

  • An SS, Friedl T, Hegewald E (1999) Phylogenetic relationships of Scenedesmus and Scenedesmus-like coccoid green algae as inferred from ITS-2 rDNA sequence comparisons. Plant Biol 1:418–429

    Article  Google Scholar 

  • Besendahl A, Qiu YL, Lee J, Palmer JD, Bhattacharya D (2000) The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I intron. Curr Genet 37:12–23

    Article  CAS  PubMed  Google Scholar 

  • Buchheim MA, Sutherland DM, Schleicher T, Forster F, Wolf M (2012) Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2. Ann Bot 109:109–116

    Article  CAS  PubMed  Google Scholar 

  • Caisová L, Marin B, Melkonian M (2013) A consensus secondary structure of ITS2 in the Chlorophyta identified by phylogenetic reconstruction. Protist 164:482–496

    Article  PubMed  Google Scholar 

  • Cheng J, Zeng X, Ran G, Liu Z (2013) CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes. BMC Bioinform 14:95. https://doi.org/10.1186/1471-2105-14-95

    Article  Google Scholar 

  • Chodat R (1926) Scenedesmus. Étude de génétique, de systématique expérimentale et d’hydrobiologie. Rev Hydrobiol 3:71–258

    Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Cambiaire JC, Otis C, Lemieux C, Turmel M (2006) The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands. BMC Evol Biol 6:37. https://doi.org/10.1186/1471-2148-6-37

    Article  PubMed  PubMed Central  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eliáš M, Němcová Y, Škaloud P, Neustupa J, Kaufnerová V, Šejnohová L (2010) Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore. Int J Syst Evol Microbiol 60:1224–1235

    Article  PubMed  Google Scholar 

  • Fučíková K, Lewis PO, Lewis LA (2016) Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution. Mol Phylogenet Evol 98:176–183

    Article  PubMed  Google Scholar 

  • Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31:439–441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guiry MD, Guiry GM (2016) AlgaeBase. World-wide electronic publication. National University of Ireland, Galway

    Google Scholar 

  • He LJ, Lou SL, Zhang F, Yang SJ, Zhang C, Lin XZ, Yang LH (2016) The complete mitochondrial DNA sequence of the green algae Hariotina sp. F30 (Scenedesmaceae, Sphaeropleales, Chlorophyceae). Mitochondrial DNA Part B: Resour 1:132–133

    Article  Google Scholar 

  • Hegewald E (1978) Eine neue Unterteilung der Gattung Scenedesmus Meyen. Nova Hedwig 30:343–376

    Article  Google Scholar 

  • Hegewald E (2000) New combinations in the genus Desmodesmus (Chlorophyceae, Scenedesmaceae). Algol Stud 96:1–18

    Google Scholar 

  • Hegewald E, Silva PC (1988) Annotated catalogue of Scenedesmus and nomenclaturally related genera including original descriptions and figures. Bibl Phycol 80:1–587

    Google Scholar 

  • Hegewald E, Wolf M, Keller A, Friedl T, Krienitz L (2010) ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus. Phycologia 49:325–335

    Article  CAS  Google Scholar 

  • Hilker R, Sickinger C, Pedersen CNS, Stoye J (2012) UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics 28:2509–2511

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M (2008) ITS2 data corroborate a monophyletic chlorophycean DO-group (Spaheropleales). BMC Evol Biol 8:218. https://doi.org/10.1186/1471-2148-8-218

    Article  PubMed  PubMed Central  Google Scholar 

  • Kessler E, Schäfer M, Hümmer C, Kloboucek A, Huss VAR (1997) Physiological, biochemical, and molecular characters for the taxonomy of the subgenera of Scenedesmus (Chlorococcales, Chlorophyta). Bot Acta 110:244–250

    Article  Google Scholar 

  • Krienitz L, Bock C (2012) Present state of the systematic of planktonic coccoid green algae of inland waters. Hydrobiologia 698:295–326

    Article  Google Scholar 

  • Lohse M, Drechsel O, Bock R (2007) Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–274

    Article  CAS  PubMed  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  CAS  PubMed  Google Scholar 

  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, HÓ§hna S et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542

    Article  PubMed  PubMed Central  Google Scholar 

  • Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trainor FR, Cain JR, Shubert EL (1976) Morphology and nutrition of the colonial green alga Scenedesmus: 80 years later. Bot Rev 42:5–25

    Article  Google Scholar 

  • Turmel M, Otis C, Lemieux C (2015) Dynamic evolution of the chloroplast genome in the green algal classes Pedinophyceae and Trebouxiophyceae. Genome Biol Evol 7:2062–2080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Hannen EJ, Fink P, Lürling M (2002) A revised secondary structure model for the internal transcribed spacer 2 of the green algae Scenedesmus and Desmodesmus and its implication for the phylogeny of these algae. Eur J Phycol 37:203–208

    Article  Google Scholar 

  • Vanormelingen P, Hegewald E, Braband A, Kitschke M, Friedl T, Sabbe K, Vyverman W (2007) The systematics of small spineless Desmodesmus species, D. costato-granulatus (Sphaeropleales, Chlorophyceae), based on ITS2 rDNA sequence analyses and cell wall morphology. J Phycol 43:378–396

    Article  CAS  Google Scholar 

  • Wolf M, Buchheim M, Hegewald E, Krienitz L, Hepperle D (2002) Phylogenetic position of the Sphaeropleaceae (Chlorophyta). Plant Syst Evol 230:161–171

    Article  CAS  Google Scholar 

  • Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by Demonstration Project of Marine Economy Innovative Development Project (Nos. 12PYY001SF08, 16PYY005SF09), Natural Science Foundation of Fujian Province (No. 2016J05100), Xiamen Southern Oceanographic Center (No. 14CZP028HJ02) and the Xiamen Science and Technology Project (No. 3502Z20172017).

Author information

Author notes

  1. Lijuan He and Zhaokai Wang have contributed equally to this work.

Authors and Affiliations

  1. Xiamen Overseas Chinese Subtropical Plant Introduction Garden, Xiamen, Fujian, China

    Lijuan He

  2. Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, China

    Zhaokai Wang, Xiangzhi Lin & Fan Hu

  3. Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, Guangdong, China

    Sulin Lou

Authors
  1. Lijuan He
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhaokai Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sulin Lou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiangzhi Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fan Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fan Hu.

Ethics declarations

Conflict of interest

Lijuan He declares that she does not have conflict of interest. Zhaokai Wang declares that he does not have conflict of interest. Sulin Lou declares that she does not have conflict of interest. Xiangzhi Lin declares that he does not have conflict of interest. Fan Hu declares that he does not have conflict of interest.

Research involving with human and animal participants

This article does not contain any animal or human subjects. The research material is not in the endangered species list.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 26 KB)

Supplementary material 2 (DOCX 26 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

He, L., Wang, Z., Lou, S. et al. The complete chloroplast genome of the green algae Hariotina reticulata (Scenedesmaceae, Sphaeropleales, Chlorophyta). Genes Genom 40, 543–552 (2018). https://doi.org/10.1007/s13258-018-0652-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-018-0652-x

Keywords

Search

Navigation