Conservation Genetics Resources

, Volume 11, Issue 3, pp 249–252 | Cite as

Characterization of the complete chloroplast genomes of the endangered shrub species Prunus mongolica and Prunus pedunculata (Rosales: rosaceae)

  • Yi-Zhong Duan
  • Ye-Hua ShenEmail author
  • Fu-Ren Kang
  • Jian-Wu Wang
Technical Note


Prunus mongolica and Prunus pedunculata are two shrub species with high ecological and economic values, and have experienced population decline and range contraction during the past decades. To promote their conservation and restoration, complete chloroplast (cp) genomes were assembled using next-generation sequencing technology in this study. The cp genomes of P. mongolica and P. pedunculata were 158,039 and 157,851 bp in length, respectively, and both comprise a pair of inverted repeat regions, separated by a large single-copy region and a small single-copy region. A total of 111 gene species were annotated for both species, including 78 protein-coding (PCG), 29 tRNA and four rRNA gene species; nineteen gene species are completely or partially duplicated within the IR regions. P. mongolica was found to be closely related to the congeners P. kansuensis and P. persica, while P. pedunculata to P. humilis and P. mume.


Chloroplast genome Endangered species Genome assembly Illumina sequencing MITObim 



This work was supported by the National Natural Science Foundation of China (Grant No. 41601059) and the Postdoctoral Science Foundation of Northwest University.

Supplementary material

12686_2017_979_MOESM1_ESM.doc (39 kb)
Supplementary material 1 (DOC 39 KB)


  1. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. CrossRefGoogle Scholar
  2. Bruun-Lund S, Clement WL, Kjellberg F, Rønsted N (2017) First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae). Mol Phylogenet Evol 109:93–104. CrossRefGoogle Scholar
  3. Choi KS, Son O, Park S (2015) The chloroplast genome of Elaeagnus macrophylla and trnH duplication event in Elaeagnaceae. PLoS ONE 10:e0138727. CrossRefGoogle Scholar
  4. Chu J, Xu X, Zhang Y (2013) Production and properties of biodiesel produced from Amygdalus pedunculata Pall. Bioresour Technol 134:374–376. CrossRefGoogle Scholar
  5. Chu J, Li Y, Zhang L, Li B, Gao M, Tang X, Ni J, Xu X (2017) Potential distribution range and conservation strategies for the endangered species Amygdalus pedunculata. Biodivers Sci 25:799–806. CrossRefGoogle Scholar
  6. Feng Y, Liu T, Wang X-Y, Li B-B, Liang C-L, Cai Y-L (2017) Characterization of the complete chloroplast genome of the Chinese cherry Prunus pseudocerasus (Rosaceae). Conservation Genet Resour. Google Scholar
  7. Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads: a baiting and iterative mapping approach. Nucl Acids Res 41:e129. CrossRefGoogle Scholar
  8. Jansen RK, Saski C, Lee S-B, Hansen AK, Daniell H (2011) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28:835–847. CrossRefGoogle Scholar
  9. Li X, Ma S (2017) Genetic variation structure of the endangered plant Amygdalus pedunculata. Acta Bot Boreal-Occident Sin 37:1278–1285. Google Scholar
  10. 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 13:715. CrossRefGoogle Scholar
  11. Lohse M, Drechsel O, Kahlau S, Bock R (2013) Organellar genomeDRAW: a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucl Acids Res 41:W575-W581. CrossRefGoogle Scholar
  12. Lu L, Bartholomew B (2003) Amygdalus Linnaeus, Sp. Pl. 1: 472. 1753. Flora China 9:391–395Google Scholar
  13. Ma S, Nie Y, Duan X, Yu C, Wang R (2015) The potential distribution and population protection priority of Amygdalus mongolica. Acta Ecol Sin 35:2960–2966. Google Scholar
  14. 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. CrossRefGoogle Scholar
  15. Zhang J, Wang J, Li H, Zhang H, Wang Y (2012) Genetic diversity of different eco-geographical populations in endangered plant Prunus mongolica by ISSR markers. Acta Ecol Sin 32:4443–4452. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Yi-Zhong Duan
    • 1
    • 2
    • 3
  • Ye-Hua Shen
    • 1
    Email author
  • Fu-Ren Kang
    • 2
    • 3
  • Jian-Wu Wang
    • 2
    • 3
  1. 1.College of Chemistry and Materials SciencesNorthwest UniversityXi’anPeople’s Republic of China
  2. 2.College of Life SciencesYulin UniversityYulinPeople’s Republic of China
  3. 3.Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining AreaYulinPeople’s Republic of China

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