Conservation Genetics Resources

, Volume 10, Issue 2, pp 209–212 | Cite as

Characterization of the complete chloroplast genomes of two sister species of Paeonia: genome structure and evolution

  • Huie Li
  • Qiqiang Guo
  • Weilie Zheng
Technical Note


The two tree peony species, namely, Paeonia ludlowii (Stern & G. Taylor) D. Y. Hong and P. delavayi Franch, belongs to the section Moutan Paeonia (Paeoniaceae). They are the only sources of yellow pigment in tree peony cultivar breeding. P. ludlowii has been listed as “critically endangered”, whereas P. delavayi has been listed as “near threatened” species according to the China Species Red List. The complete chloroplast genome sizes of P. ludlowii and P. delavayi are 152,687 and 154,405 bp respectively. Both contain a 17,056 bp long small single copy region (SSC). The large single copy region (LSC) in P. ludlowii is 84,613 bp, whereas the inverted repeat regions (IRs) are 25,644 bp. In addition, LSC in P. delavayi is 86,142 bp, whereas the IRs is 25,650 bp. The genomes of the two species encode the same set of 134 genes, including 86 protein-coding genes, 8 ribosomal RNA genes and 40 transfer RNA genes. Phylogenetic analysis revealed that all five Paeonia species clustered together, and P. ludlowii and P. delavayi are most closely related to each other. These newly characterized chloroplast genomes will provide essential data for the further conservation of P. ludlowii and P. delavayi.


Paeonia ludlowii Paeonia delavayi Endangered species Endemic species Chloroplast genome Phylogeny 



This research was financially supported by Scientific Research Foundation for Advanced Talent of Guizhou University (2016-43), China.


  1. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Doyle J, Doyle J (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  3. Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach Nucleic Acids Res. doi: 10.1093/nar/gkt371 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Hao HP, He Z, Li H, Shi L, Tang YD (2014) Effect of root length on epicotyl dormancy release in seeds of Paeonia ludlowii. Tibetan Peony Ann Bot 113:443–452. doi: 10.1093/aob/mct273 CrossRefPubMedGoogle Scholar
  5. Hong D (1997) Paeonia (Paeoniaceae) in Xizang (Tibet). Novon 156–161Google Scholar
  6. Hong D, Pan K, Hong Y (1998) Taxonomy of the Paeonia delavayi complex (Paeoniaceae). Ann Mo Bot Gard 85:554–564. doi: 10.2307/2992016 CrossRefGoogle Scholar
  7. Kearse M et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi: 10.1093/bioinformatics/bts199 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Li C et al (2009) Flavonoid composition and antioxidant activity of tree peony (Paeonia Section Moutan) yellow flowers. J Agric Food Chem 57:8496–8503. doi: 10.1021/jf902103b CrossRefPubMedGoogle Scholar
  9. Li H, Guo Q, Zheng W (2016) The complete chloroplast genome of Cupressus gigantea, an endemic conifer species to Qinghai-Tibetan Plateau. Mitochondr DNA Part A 27:3743–3744. doi: 10.3109/19401736.2015.1079885 CrossRefGoogle Scholar
  10. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. doi: 10.1093/molbev/mst197 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Wang S, Xie Y (2004) China species red list, vol 8. Higher Education Press, BeijingGoogle Scholar
  12. Wang SQ, Li HM, Wang L, Cheng J, Tang L (2012) On the meiosis in Paeonia ludlowii (Stern & Taylor) D. Y. Hong, an endangered species of SE Tibet, PR China. Wulfenia 19:97–106Google Scholar
  13. Yang J-B, Li D-Z, Li H-T (2014) Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour 14:1024–1031. doi: 10.1111/1755-0998.12251 CrossRefPubMedGoogle Scholar
  14. Zhang J-M, Liu J, Sun H-L, Yu J, Wang J-X, Zhou S-L (2011) Nuclear and chloroplast SSR markers in Paeonia delavayi (Paeoniaceae) and cross-species amplification in P. ludlowii. Am J Bot 98:E346–E348. doi: 10.3732/ajb.1100240 CrossRefPubMedGoogle Scholar
  15. Zhao X, Zhou Z-Q, Lin Q-B, Pan K-Y, Li M-Y (2008) Phylogenetic analysis of Paeonia sect. Moutan (Paeoninceae) based on multiple DNA fragments morphological data. J Syst Evol 46:563–572. doi: 10.3724/sp.j.1002.2008.06197 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.College of AgricultureGuizhou UniversityGuiyangPeople’s Republic of China
  2. 2.Institute for Forest Resources & Environment of GuizhouGuizhou UniversityGuiyangPeople’s Republic of China
  3. 3.Institute of Tibet Plateau EcologyNyingchiPeople’s Republic of China
  4. 4.Tibet Agricultural and Animal Husbandry CollegeNyingchiPeople’s Republic of China

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