Skip to main content
SpringerLink
Log in

The complete chloroplast genome of a rare candelabra primrose Primula stenodonta (Primulaceae)

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

The whole chloroplast genome (cp genome) of Primula stenodonta was sequenced using an Illumina platform. The cp genome is 150,785 bp in size, and exhibits a typical bicyclic and quadripartite structure, including a pair of inverted repeat regions (IRs) of 25,182 bp that are separated by large and small single copy regions of 82,682 and 17,739 bp, respectively. A total of 131 genes were identified, including 86 protein-coding genes (PCG), 37 tRNA genes, and eight ribosomal RNA (rRNA) genes. Among them, 18 genes occur in IRs, containing seven PCG, seven tRNA genes and four rRNA genes. The overall AT content of P. stenodonta cp genome is 62.9%, and the corresponding values of the LSC, SSC and IR regions are 65, 69.8 and 57%, respectively. The phylogenetic analysis suggested that the sampled Primula species formed a monophyletic clade, and P. stenodonta is closely related to Primula poissonii.

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

References

  • Hu CM (1990) Primulaceae. In: Chen FW, Hu CM (eds) Flora Reipublicae Popularis Sinicae, vol 59. Science Press, Beijing, pp 111–128

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu TJ, Zhang CY, Yan HF, Zhang L, Ge XJ, Hao G (2016) Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus. PeerJ 4:e2101. doi:10.7717/peerj.2101

    Article  PubMed  PubMed Central  Google Scholar 

  • Lohse M, Drechsel O, Kahlau S, Bock R (2013) Organellar genome DRAW: a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41(W1):W575–W581

    Article  PubMed  PubMed Central  Google Scholar 

  • Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. In: proceedings of the gateway computing environments workshop (GCE). 14 Nov. 2010, New Orleans, pp 1–8

  • Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15(1):8–15

    Article  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, Li DZ, Li HT (2014) Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Res 14(5):1024–1031

    CAS  Google Scholar 

  • Zhang T, Zeng CX, Yang JB, Li HT, Li DZ (2016) Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs. J Syst Evol 54:219–227

    Article  Google Scholar 

Download references

Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (31500173, 31570222), Natural Science Foundation of Guangdong Province (2014A030310120) and the Science and Technology Program of Guangzhou, China (201607010281).

Author information

Authors and Affiliations

  1. Guangdong Institute of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou, 510520, China

    Cai-Yun Zhang

  2. College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China

    Tong-Jian Liu & Gang Hao

  3. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China

    Hai-Fei Yan & Xue-Jun Ge

Authors
  1. Cai-Yun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tong-Jian Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hai-Fei Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xue-Jun Ge
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gang Hao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hai-Fei Yan.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Figure S1 Phylogenetic position of Primula stenodonta. (DOCX 43 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, CY., Liu, TJ., Yan, HF. et al. The complete chloroplast genome of a rare candelabra primrose Primula stenodonta (Primulaceae). Conservation Genet Resour 9, 123–125 (2017). https://doi.org/10.1007/s12686-016-0637-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-016-0637-5

Keywords

Search

Navigation