Conservation Genetics Resources

, Volume 9, Issue 1, pp 55–58 | Cite as

Characterization of the complete chloroplast genome of an endangered species dwarf birch (Betula nana L.)

  • Yiheng Hu
  • Xi Chen
  • Tao Zhou
  • Na Hou
  • Peng ZhaoEmail author
Technical Note


Betula nana L. is a deciduous shrub belonging to the Betulaceae family, which is recorded as endangered species in the Red List. The complete chloroplast genome of B. nana was reported in this study. The size of the B. nana chloroplast genome is 160,579 bp, with an average GC content of 36.1 %. This circular molecule has a typical quadripartite structure containing a large single copy region of 89,492 bp, a small single copy region of 19,343 bp, and two inverted repeat regions of 25,872 bp. It encodes an identical set of 114 unique genes, including 79 protein coding, 31 transfer RNA and 4 ribosomal RNA genes. The total of 20 genes were duplicated in the inverted repeats. A maximum likelihood phylogenetic tree supported that the chloroplast genome of B. nana is closely related to that of Ostrya rehderiana.


Betula nana Complete chloroplast genome Endangered species Phylogenetic 



This work was supported by the National Natural Science Foundation of China (No. 41471038, No. 31200500, and No. J1210063), the Program for Excellent Young Academic Backbones funding by Northwest University, Changjiang Scholars and Innovative Research Team in University (IRT1174), Northwest University Training Programs of Innovation and Entrepreneurship for graduates and undergraduates (No. 2015159 and No. 2016171), The Talent Team Construction Project of Guizhou Province, 20034009, Guizhou Science and Research Organization Serving Enterprises (20154010).


  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Pyshkin AV (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477CrossRefPubMedPubMedCentralGoogle Scholar
  2. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14(6):1147–1159CrossRefPubMedPubMedCentralGoogle 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 41:e129CrossRefPubMedPubMedCentralGoogle Scholar
  4. Jansen RK, Cai Z, Raubeson LA, Daniell H, Leebens-Mack J, Müller KF, Lee SB (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Nat Acad Sci USA 104(49):19369–19374CrossRefPubMedPubMedCentralGoogle Scholar
  5. Järvinen P, Palmé A, Morales LO, Lännenpää M, Keinänen M, Sopanen T, Lascoux M (2004) Phylogenetic relationships of Betula species (Betulaceae) based on nuclear ADH and chloroplast matK sequences. Am J Bot 91(11):1834–1845CrossRefPubMedGoogle Scholar
  6. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780CrossRefPubMedPubMedCentralGoogle Scholar
  7. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359CrossRefPubMedPubMedCentralGoogle Scholar
  8. 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. Nucleic acids Res 41:W575–W581CrossRefPubMedPubMedCentralGoogle Scholar
  9. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313CrossRefPubMedPubMedCentralGoogle Scholar
  10. Stritch L (2014) Betula nana. The IUCN red list of threatened species 2014:e.T194495A2341542Google Scholar
  11. Wang N, Thomson M, Bodles WJA, Crawford RM, Hunt HV, Featherstone AW, Pellicer J, Buggs RJ (2013) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol 22(11):3098–3111CrossRefPubMedGoogle Scholar
  12. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Yiheng Hu
    • 1
  • Xi Chen
    • 1
  • Tao Zhou
    • 1
  • Na Hou
    • 2
  • Peng Zhao
    • 1
    Email author
  1. 1.Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life SciencesNorthwest UniversityXi’anChina
  2. 2.Guizhou Academy of ForestryGuiyangChina

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