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Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii

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Abstract

The complete chloroplast genome sequence of Korean Cymbidium goeringii acc. smg222 was analyzed. Based on a comparison with Chinese C. goeringii, losses of nine ndh subunits (ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhH, ndhJ, and ndhK), three protein-coding genes (ycf 1-like, ycf 15, and ycf 68), six transfer RNAs, and one conserved open reading frame (orf 42). In addition, 219 InDels (insertion or deletion) and 171 simple sequence repeats were observed. Twenty-Five of which InDel markers have been evaluated, that useful for distinguishing Korean and Chinese Cymbidium associations based on the polymorphisms of chloroplast genomes between Korean Cymbidium goeringii acc. smg222 and Chinese C. goeringii and evaluation of genetic diversity. Finally, the phylogenetic relationships of the 39 Korean and 22 Chinese species was constructed based on the five InDel markers of them and obtained high support, indicating that our data may be useful in resolving relationships in this genus. The information about chloroplast DNA structure and gene variants of C. goeringii acc. smg222 chloroplast genome will provide sufficient phylogenetic information for resolving evolutionary relationships. The molecular markers developed in here will contribute to further research of Cymbidium species and conservation of endemic Cymbidium species.

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References

  • Asaf S, Khan AL, Khan MA, Imran QH, Kang SM, Al-Hosni K, Jeong EJ, Lee KE, Lee IJ (2017) Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species. PLoS ONE 12:e0182281

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156(2):847–854

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chang CC, Chaw SM (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol 23(2):279–291

    Article  CAS  PubMed  Google Scholar 

  • Choi SH, Kim MJ, Lee JS, Ryu KH (2006) Genetic diversity and phylogenetic relationships among and within species of oriental cymbidiums based on RAPD analysis. Sci Hortic 108(1):79–85

    Article  CAS  Google Scholar 

  • Delannoy E, Fujii S, des FrancsSmall CC, Brundrett M, Small I (2011) Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes. Mol Biol Evol 28(7):2077–2086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Do HDK, Kim JS, Kim JH (2013) Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae). Gene 530(2):229–235

    Article  CAS  PubMed  Google Scholar 

  • Dong W, Liu J, Yu J, Wang L, Zhou S (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7(4):e35071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong W, Xu C, Cheng T, Zhou S (2013) Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales. PLoS ONE 8(10):e77965

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du Puy D, Cribb P, Tibbs M (2007) The genus Cymbidium. Royal Botanic Gardens, Kew

    Google Scholar 

  • Funk HT, Berg S, Krupinska K, Maier UG, Krause K (2007) Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol 7(1):45

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gao L, Yi X, Yang YX, Su YJ, Wang T (2009) Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol 9(1):130

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gray MW, Lang BF, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Brossard N, Delage E, Tim GL, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G (1998) Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res 26(4):865–878

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol 28(1):583–600

    Article  CAS  PubMed  Google Scholar 

  • Jo YD, Park J, Kim J, Song W, Hur CG, Lee YH, Kang BC (2011) Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep 30(2):217–229

    Article  CAS  PubMed  Google Scholar 

  • Kim K, Lee SC, Lee J, Lee HO, Joh HJ, Kim NH, Pakr HS, Yang TJ (2015) Comprehensive survey of genetic diversity in chloroplast genomes and 45S nrDNAs within Panax ginseng species. PLoS ONE 10(6):e0117159

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28(14):1838–1844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X (2012) CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genom 13(1):715

    Article  CAS  Google Scholar 

  • Liu X, Huang Y, Li F, Xu C, Chen K (2014) Genetic diversity of 129 spring orchid (Cymbidium goeringii) cultivars and its relationship to horticultural types as assessed by EST-SSR markers. Sci Horticult 174:178–184

    Article  Google Scholar 

  • Moe KT, Zhao W, Song HS, Kim YH, Chung JW, Cho YI, Park PH, Park HS, Chae SC, Park YJ (2010) Development of SSR markers to study diversity in the genus Cymbidium. Biochem Syst Ecol 38(4):585–594

    Article  CAS  Google Scholar 

  • Obara-Okeyo P, Kako S (1998) Genetic diversity and identification of Cymbidium cultivars as measured by random amplified polymorphic DNA (RAPD) markers. Euphytica 99(2):95–101

    Article  CAS  Google Scholar 

  • Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7(1):84

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Price A, Garhyan J, Gibas C (2017) The impact of RNA secondary structure on read start locations on the Illumina sequencing platform. PLoS ONE 12(2):e0173023

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genom 8(1):174

    Article  CAS  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(suppl 2):W686–W689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song Y, Dong W, Liu B, Xu C, Yao X, Gao J, Corlett RT (2015) Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Front Plant Sci 6:662

    PubMed  PubMed Central  Google Scholar 

  • Suo Z, Zhang C, Zheng Y, He L, Jin X, Hou B, Li J (2012) Revealing genetic diversity of tree peonies at micro-evolution level with hyper-variable chloroplast markers and floral traits. Plant Cell Rep 31(12):2199–2213

    Article  CAS  PubMed  Google Scholar 

  • Wang HZ, Wang YD, Zhou XY, Ying QC, Zheng KL (2004) Analysis of genetic diversity of 14 species of Cymbidium based on RAPDs and AFLPs. Shi Yan Sheng Wu Xue Bao 37(6):482–486

    CAS  PubMed  Google Scholar 

  • Wang HZ, Wu ZX, Lu JJ, Shi NN, Zhao Y, Zhang ZT, Liu JJ (2009) Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers. Genetica 136(3):391–399

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Park SY, Lee AR, Jang SG, Im DE, Jun TH, Lee JH, Chung JW, Kwon SW (2018) Next-generation sequencing yields the complete chloroplast genome of C. goeringii acc. smg222 and phylogenetic analysis. Mitochondr DNA B 3(1):215–216

    Article  Google Scholar 

  • Wicke S, Schneeweiss GM, Müller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76(3–5):273–297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolfe KH, Morden CW, Palmer JD (1992) Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci 89(22):10648–10652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu FH, Chan MT, Liao DC, Hsu CT, Lee YW, Daniell H, Duval MR, Lin CS (2010) Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol 10(1):68

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255

    Article  CAS  PubMed  Google Scholar 

  • Yang JB, Tang M, Li HT, Zhang ZR, Li DZ (2013) Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evol Biol 13(1):84

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) provided this research through Technology Commercialization Support Program. The finance was contributed by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (815004–03).

Funding

This work was supported by grants from Ministry of Agriculture, Food and Rural Affairs of Korea (MAFRA).

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Author notes

  1. Heng Wang and So-Yeon Park are contributed equally.

Authors and Affiliations

  1. Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea

    Heng Wang, So-Yeon Park, Su-Hyang Song, Mar-Lar San, Yong-Chul Kim & Soon-Wook Kwon

  2. State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Heng Wang

  3. Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea

    Tae-Ho Ham & Joohyun Lee

  4. Department of Agricultural Science, Korea National Open University, Seoul, 03087, Republic of Korea

    Tae-Ho Ham & Tae-Sung Kim

  5. Saemangeum BioCenter Co, 1044 Heomi-ro, Daeya-myeon, Gunsan, 54061, Republic of Korea

    Dong-Yong Kim

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  1. Heng Wang
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Contributions

HW, SYP and SWK developed ideas, designed and performed all experiments, and wrote the manuscript. YCK and DYK produced all cymbidium materials. THH, JL, and TSK analyzed the sequencing dates. SHS and SML analyzed the InDel markers for experiments. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Soon-Wook Kwon.

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Conflict of interest

All the authors declare that they have on conflict of interest in the publication.

Additional information

The complete chloroplast genome sequence of C. goeringii acc. smg222 has been deposited at GenBank under the accession number MF421552.

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Wang, H., Park, SY., Song, SH. et al. Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii. 3 Biotech 10, 29 (2020). https://doi.org/10.1007/s13205-019-2020-1

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