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

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.

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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.

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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).

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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.

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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.

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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

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

Keywords

  • Cupressaceae
  • Genetic structure
  • Germplasm resources
  • Illumina sequencing
  • Metasequoia glyptostroboides