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Conservation Genetics Resources

, Volume 10, Issue 3, pp 367–370 | Cite as

Characterization of the complete chloroplast genome of black cherry (Prunus serotina Ehrh.)

  • Aiping Luan
  • Aiping Gao
  • Junhu He
  • Guiqi Bi
  • Yehua HeEmail author
Technical Note

Abstract

Prunus serotina, with high wildlife value, is a tree with edible fruits that is native to North America. In this study, the complete chloroplast (cp) genome of Prunus serotina (Amygdaleae) was determined through Illumina sequencing method. The complete chloroplast genome of P. serotina was 158,788 bp in length and contained a pair of IR regions (26,294 bp) separated by a small single copy region (18,911 bp) and a large single copy region (82,048 bp). The cp genome of P. serotina encoded 130 genes including 84 protein-coding genes, 37 tRNA genes and eight ribosomal RNA genes. The overall GC content of P. serotina cp genome is 36.6%. By phylogenetic analysis using Bayesian method, P. serotina showed the closest relationship with Sohing (Prunus nepalensis). This complete chloroplast genomes can be subsequently used for population genomic studies of P. serotina and provide valuable insight into its in situ and ex situ conservation.

Keywords

Prunus serotina Chloroplast genome Illumina sequencing Phylogenetic analysis 

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 31572089, No. 30971984).

Compliance with ethical standards

Conflict of interest

The authors have declared that no competing interests exist.

References

  1. Bankevich A et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology 19(5):455–477CrossRefPubMedPubMedCentralGoogle Scholar
  2. Fowells HA (1965) Silvics of forest trees of the United States. Agriculture Handbook US Department of Agriculture, Washington, p 271Google Scholar
  3. Fresnedo-Ramírez J, Segura S, Muratalla-Lúa A (2011) Morphovariability of capulín (Prunus serotina Ehrh.) in the central-western region of Mexico from a plant genetic resources perspective. Genet Resour Crop Evol 58(4):481–495CrossRefGoogle Scholar
  4. 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 41(13):e129CrossRefPubMedPubMedCentralGoogle Scholar
  5. Horsley SB, Meinwald J (1981) Glucose-1-benzoate and prunasin from Prunus serotina. Phytochemistry 20(5):1127–1128CrossRefGoogle Scholar
  6. Huang DI, Cronk QC (2015) Plann: a command-line application for annotating plastome sequences. Appl Plant Sci 3(8):1500026CrossRefGoogle Scholar
  7. Jansen RK et al (2010) 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(1):835–847CrossRefPubMedPubMedCentralGoogle Scholar
  8. Krochmal A, Walters RS, Doughty RM (1969) A guide to medicinal plants of Appalachia. Research Papers. Northeastern Forest Experiment Station NE-138Google Scholar
  9. Lartillot N, Lepage T, Blanquart S (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25(17):2286–2288Google Scholar
  10. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52(5):267–274CrossRefPubMedGoogle Scholar
  11. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964CrossRefPubMedPubMedCentralGoogle Scholar
  12. Ruby J, Graham PB, Joseph LD (2013) PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3: Genes Genomes Genet 3(5):865–880CrossRefGoogle Scholar
  13. Wick RR et al (2015) Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31(20):3350–3352CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Aiping Luan
    • 1
    • 2
  • Aiping Gao
    • 2
  • Junhu He
    • 2
  • Guiqi Bi
    • 3
  • Yehua He
    • 1
    Email author
  1. 1.College of HorticultureSouth China Agricultural UniversityGuangzhouChina
  2. 2.Institute of Tropical Crop GermplasmChinese Academy of Tropical Agricultural SciencesDanzhouChina
  3. 3.College of Marine Life SciencesOcean University of ChinaQingdaoChina

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