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Conservation Genetics Resources

, Volume 9, Issue 3, pp 415–418 | Cite as

The complete chloroplast genome of a vulnerable species Champereia manillana (Opiliaceae)

  • Guan-Song Yang
  • Yin-Huan Wang
  • Yue-Hua WangEmail author
  • Shi-Kang ShenEmail author
Technical Note

Abstract

Champereia manillana (Bl.) Merr. is a vulnerable plant from the family Opiliaceae. The complete chloroplast genome (plastome) of Opiliaceae family was sequenced for the first time. The plastome of C. manillana was 147,461 bp in length. It was consisted of a large single copy (LSC) region (83,505 bp) and a small single copy (SSC) region (7,806 bp), which were separated by two inverted repeats (IRs, 28,075 bp). This plastome contained 101 different genes, including 67 protein-coding genes (PCGs), 30 tRNA genes and four rRNA genes. The overall GC content was 37.4%. Furthermore, phylogenetics analysis of 4 species in the Santalales was also conducted. The whole chloroplast genome of this species will be useful for the future plant evolutionary, phylogeny and genomic studies in the family Opiliaceae.

Keywords

Champereia manillana Chloroplast genome Vulnerable species 

Notes

Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (31360074).The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

References

  1. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  2. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780CrossRefPubMedPubMedCentralGoogle Scholar
  3. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649CrossRefPubMedPubMedCentralGoogle Scholar
  4. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9(4):357–359CrossRefPubMedPubMedCentralGoogle Scholar
  5. Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomedraw—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41(W1):W575–W581CrossRefPubMedPubMedCentralGoogle Scholar
  6. Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Paper presented at the Gateway Computing Environments Workshop (GCE), New Orleans, LA, 14 Nov. doi:10.1109/GCE.2010.5676129Google Scholar
  7. Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689CrossRefPubMedPubMedCentralGoogle Scholar
  8. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313CrossRefPubMedPubMedCentralGoogle Scholar
  9. Wick RR, Schultz MB, Zobel J, Holt KE (2015) Bandage: interactive visualisation of de novo genome assemblies. Bioinformatics 31(20):3350–3352CrossRefPubMedPubMedCentralGoogle Scholar
  10. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255CrossRefPubMedGoogle Scholar
  11. Xu LR, Chen TC, Zhu XY, Huang PH, Wei Z, Sa R, Zhang DX, Bao BJ, Wu TL, Sun H, Gao XF, Liu YH, Chang ZY, Li JQ, Zhang ML, Podlech D, Ohashi H, Larsen K, Welsh SL, Vincent MA, Gilbert MG, Pedley L, Schrire BD, Yakovlev GP, Thulin M, Nielsen IC, Choi BH, Turland NJ, Polhill RM, Larsen SS, Hou D, Iokawa Y, Wilmot-Dear CM, Kenicer G, Nemoto T, Lock JM, Salinas AD, Kramina TE, Brach AR, Bartholomew B, Sokoloff DD (2010) Opiliaceae. In: Wu ZY, Raven PH (eds) Flora of China, vol 10. Science Press & Missouri Botanical Garden Press, Beijing and St. LouisGoogle Scholar
  12. Yang JB, Li DZ, Li HT (2014) Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour 14(5):1024–1031PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  1. 1.School of Life SciencesYunnan UniversityKunmingChina

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