Skip to main content

Advertisement

SpringerLink
Log in

Novel 28 microsatellite loci using high-throughput sequencing for an endangered species on Metasequoia glyptostroboides (Cupressaceae)

  • Short Communication
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Metasequoia glyptostroboides is a living fossil and an endangered species listed in the International Union for Conservation of Nature (IUCN). Distinguishing the genotypes of all wild individuals of M. glyptostroboides is important to delimit management units and key germplasm resources. We characterized 28 novel polymorphic microsatellite loci using a streptavidin–biotin microsatellite-enriched library and Illumina high-throughput sequencing. Characteristics of each locus were tested using 140 individuals collected from five natural populations of M. glyptostroboides. The number of alleles per locus ranged from 3 to 20, with a mean number of about 8 alleles. The observed and expected heterozygosities in each population ranged from 0.0000 to 1.0000 and from 0.0000 to 0.8958, respectively. Four to nine loci were cross-amplified successfully in seven species of Cupressaceae. The novel SSR markers will provide a toolkit for DNA identification of all of the extant wild individuals guiding further conservation efforts of M. glyptostroboides.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Data availability

Raw sequencing data were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (BioProject ID: PRJNA578834). Sequence information for the develop primers has been deposited to NCBI, and GenBank accession numbers are provided in Table 1.

References

  1. LePage BA, Yang H, Matsumoto M (2005) The evolution and biogeographic history of Metasequoia. In: LePage BA, Williams CJ, Yang H (eds) The geobiology and ecology of Metasequoia. Springer, Heidelberg.

    Chapter  Google Scholar 

  2. Li YY, Chen XY, Zhang X, Wu TY, Lu HP, Cai YW (2005) Genetic differences between wild and artificial populations of Metasequoia glyptostroboides: implications for species recovery. Conserv Biol 19:224–231. https://doi.org/10.1111/j.1523-1739.2005.00025.x

    Article  Google Scholar 

  3. Verissimo D, MacMillan DC, Smith RJ (2011) Toward a systematic approach for identifying conservation flagships. Conserv Lett 4:1–8. https://doi.org/10.1111/j.1755-63X.2010.00151.x

    Article  Google Scholar 

  4. Santarém F, Pereira P, Saarinen J, Brito JC (2019) New method to identify and map flagship fleets for promoting conservation and ecotourism. Biol Conserv 229:113–124. https://doi.org/10.1016/j.biocon.2018.10.017

    Article  Google Scholar 

  5. Li YY, Ysang EPK, Cui MY, Chen XY (2012) Too early to call it success: an evaluation of the natural regeneration of the endangered Metasequoia glyptostroboides. Biol Conserv 150:1–4. https://doi.org/10.1016/j.biocon.2012.02.020

    Article  Google Scholar 

  6. Farjon A (2010) A handbook of the world's conifers. Brill, Leiden

    Book  Google Scholar 

  7. Spielman D, Brook BW, Frankham R (2004) Most species are not driven to extinction before genetic factors impact them. Proc Natl Acad Sci USA 101:15261–15264. https://doi.org/10.1073/pnas.0403809101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Cui MY, Yu S, Liu M, Li YY (2010) Isolation and characterization of polymorphic microsatellite markers in Metasequoia glyptostroboides (Taxodiaceae). Conserv Genet Resour 2:19–21. https://doi.org/10.1007/s12686-009-9132-6

    Article  Google Scholar 

  9. Jin YQ, Bi QW, Guan WB, Mao JF (2015) Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides. Appl Plant Sci 3:1500038. https://doi.org/10.3732/apps.1500038

    Article  Google Scholar 

  10. Fan XX, Shen L, Zhang X, Chen XY, Fu CX (2004) Assessing genetic diversity of Ginkgo biloba L. (Ginkgoaceae) populations from China by RAPD markers. Biochem Genet 42:269–278. https://doi.org/10.1023/B:BIGI.0000034431.15308.57

    Article  CAS  PubMed  Google Scholar 

  11. Magoct T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. https://doi.org/10.1093/bioinformatics/btr507

    Article  CAS  Google Scholar 

  12. Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422. https://doi.org/10.1007/s00122-002-1031-0

    Article  CAS  PubMed  Google Scholar 

  13. UCLUST version 1.2.22q. https://www.drive5.com/uclust/downloads1_2_22q.html. Accessed 20 July 2017

  14. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer 3—new capabilities and interfaces. Nucleic Acids Res 40:e115. https://doi.org/10.1093/nar/gks596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234. https://doi.org/10.1038/72708

    Article  CAS  PubMed  Google Scholar 

  16. Miller MP (1997) Tools for population genetic analyses (TFPGA) 1.3: a Windows program for the analysis of allozyme and molecular population genetic data. https://www.marksgeneticsoftware.net/tfpga.htm. Accessed 20 Jan 2019

  17. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486

    Article  Google Scholar 

  18. Rousset F (2008) GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x

    Article  PubMed  Google Scholar 

  19. van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

    Article  CAS  Google Scholar 

  20. Mao K, Milne RI, Zhang L, Peng Y, Liu J, Thomas P, Mill RR, Renner SS (2012) Distribution of living Cupressaceae reflects the breakup of Pangea. Proc Natl Acad Sci USA 109:7793–7798. https://doi.org/10.1073/pnas.1114319109

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank X.-W. Sun, X.-H. Yue, and S.-S. Wang for their supports for field surveys and laboratory experiments. We also thank Dr. S. R. Biswas and LetPub (www.letpub.com) for linguistic assistance during the preparation of this manuscript. This work was supported by the National Key Research and Development Program (2016YFC0503102) and the National Natural Science Foundation of China (31670540).

Author information

Authors and Affiliations

  1. Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Laboratory for Urban Ecology and Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China

    Jing-Wen Wang, Tong-Lei Xu, Ghenet Weldegebriel Sereke, Rong Wang & Yuan-Yuan Li

  2. Institute of Eco-Chongming (IEC), Shanghai, 200062, China

    Yuan-Yuan Li

Authors
  1. Jing-Wen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tong-Lei Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ghenet Weldegebriel Sereke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Rong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuan-Yuan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J-WW wrote the manuscript, and collected and analyzed data. T-LX and GWS contributed to collection of data and revised the manuscript. RW helped improve the design of the experiment and critically revised the manuscript. Y-YL designed the experiment and critically revised the manuscript.

Corresponding author

Correspondence to Yuan-Yuan Li.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Research involving human participants and/or plants

This research involved endangered plants; studies were supported by the projects of Ministry of Science and Technology of the People’s Republic of China and National Natural Science Foundation of China. Our sampling was permitted by Lichuan Metasequoia Management Office and Xingdoushan National Nature Reserve of China, and was in accordance with the ethical standards of the Regulations of the People’s Republic of China on Wild Plants Protection (2017 Amendment PKULAW Version) (CLI.2.304108). During sampling, we only collected leaf tissues from each sampled individual and did not cause severe damage to wild populations of Metasequoia glyptostroboides.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, JW., Xu, TL., Sereke, G.W. et al. Novel 28 microsatellite loci using high-throughput sequencing for an endangered species on Metasequoia glyptostroboides (Cupressaceae). Mol Biol Rep 47, 2991–2996 (2020). https://doi.org/10.1007/s11033-020-05303-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-020-05303-y

Keywords

Search

Navigation