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Characterization of the complete chloroplast genome of Berchemiella wilsonii var. wilsonii (Rhamnaceae), an endangered species endemic to China

Abstract

The complete chloroplast genome (plastome) of the endangered species Berchemiella wilsonii var. wilsonii (Rhamnaceae) was firstly reported in this study. The plastome of this species was 160,333 bp in length with a quadripartite structure that consisted of two inverted repeat (IR; 26,510 bp) regions separated by the large single-copy (LSC; 88,582 bp) and small single-copy (SSC; 18,731 bp) regions. The plastome comprised 112 unique genes including 78 protein-coding genes (PCGs), 30 tRNAs and four rRNAs. The overall GC content was 37.2%. Five types of 93 simple sequence repeats (SSRs) were detected in the plastome. The complete plastome of B. wilsonii var. wilsonii will provide valuable information for the conservation genetics and phylogenetics of Rhamnaceae.

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Article  PubMed  Google Scholar 

  • Fu LK, Jin JM (1992) China plant red data book—rare and endangered plant. Science Press, Beijing

    Google Scholar 

  • Kang M, Wang J, Huang H (2008) Demographic bottlenecks and low gene flow in remnant populations of the critically endangered Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) inferred from microsatellite markers. Conserv Genet 9:191–199

    Article  Google Scholar 

  • 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, Meintjes P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  PubMed  PubMed Central  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 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:W575–W581

    Article  PubMed  PubMed Central  Google Scholar 

  • Patel RK, Jain M (2012) NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Richardson JE, Fay MF, Cronk QCB, Bowman D, Chase MW (2000) A phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences. Am J Bot 87:1309–1324

    CAS  Article  PubMed  Google Scholar 

  • Richardson JE, Chatrou LW, Mols JB, Erkens RHJ, Pirie MD (2004) Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae. Philos T R Soc B 359:1495–1508

    CAS  Article  Google Scholar 

  • Ruhlman TA, Jansen RK (2014) The plastid genomes of flowering plants. In: Pal M (ed) Chloroplast Biotechnology: Methods and Protocols. Humana Press, Totowa, pp 3–38

    Chapter  Google Scholar 

  • 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–W689

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255

    CAS  Article  PubMed  Google Scholar 

  • Yang JB, Li DZ, Li HT (2014) Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour 14:1024–1031

    CAS  Article  PubMed  Google Scholar 

  • Zhang T, Zeng CX, Yang JB, Li HT, Li DZ (2016) Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs. J Syst Evol 54:219–227

    Article  Google Scholar 

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Acknowledgements

We appreciate permission to collect samples from Wuhan Botanic Garden.

Funding

This study was funded by grant from the National Natural Science Foundation of China (No. 31200172).

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Correspondence to Shu-Dong Zhang.

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The authors declare that they have no conflict of interest.

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Wang, YH., Chen, SY. & Zhang, SD. Characterization of the complete chloroplast genome of Berchemiella wilsonii var. wilsonii (Rhamnaceae), an endangered species endemic to China. Conservation Genet Resour 10, 39–41 (2018). https://doi.org/10.1007/s12686-017-0760-y

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  • DOI: https://doi.org/10.1007/s12686-017-0760-y

Keywords

  • Plastome
  • Berchemiella wilsonii var. wilsonii
  • SSR
  • Conservation
  • Rhamnaceae