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Molecular Biology Reports

, Volume 46, Issue 1, pp 1335–1341 | Cite as

Development of microsatellite markers for the seagrass Zostera japonica using next-generation sequencing

  • Xiaomei Zhang
  • Yi ZhouEmail author
  • Yu-Long Li
  • Jin-Xian LiuEmail author
Short Communication

Abstract

The seagrass Zostera japonica Asch. & Graebn. is among the few seagrass species that thrive both in temperate and tropical intertidal zones. The degradation of Z. japonica in its native range and continued expansion in some localities have raised concerns with regard to its conservation and management. Population genetic studies of Z. japonica across its biogeographic range and within meadows are scarce. Previously developed microsatellites via traditional methods are not sufficient in quantity and perform inconsistently between the temperate and tropical populations. Thus, this study aimed to develop more reliable polymorphic markers for Z. japonica using next generation sequencing. In total, 6479 sequences containing loci were identified and 1619 pairs of primers were successfully designed. Of these, 63 loci were selected for primary validation in 16 individuals from four populations, with 48 (76.2%) polymorphic loci detected. Seventeen polymorphic loci were selected for further evaluation in 62 individuals from one temperate and one tropical population. The overall probability of identity (PID) for both populations was 2.375e−22 (PIDsib = 3.557e−08). The number of alleles, and expected and observed heterozygosity in the two populations were both relatively high and not significantly different from each other. The pairwise FST = 0.232 (p < 0.0001) and Principal Coordinates Analysis both suggested a large and significant genetic divergence between the two populations. This study makes abundant molecular markers available for genetic studies in Z. japonica, and facilitates its conservation and management strategies.

Keywords

Zostera japonica NGS Microsatellites Population genetics 

Notes

Acknowledgements

The authors thank all the individuals who assisted in the collection of samples. This research was supported by the National Science & Technology Basic Work Program (2015FY110600), the NSFC-Shandong Joint Fund for Marine Science Research Centers (U1606404), the CPSF-CAS Joint Foundation for Excellent Postdoctoral Fellows (2016LH0032), the China Postdoctoral Science Foundation (2016M600562), the key Research and Development Project of Shandong Province (2017GHY15111), the Key Research Project of Frontier Sciences of CAS (QYZDB-SSW-DQC041-1), the Science and Technology Service Network Initiative of CAS (KFJ-STS-ZDTP-023), the Creative Team Project of the Laboratory for Marine Ecology and Environmental Science from the Qingdao National Laboratory for Marine Science and Technology (LMEES-CTSP-2018-1), and the Taishan Scholars Program (Distinguished Taishan Scholars).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interests.

References

  1. 1.
    Costanza R, dArge R, deGroot R, Farber S, Grasso M, Hannon B, Limburg K, Naeem S, Oneill RV, Paruelo J, Raskin RG, Sutton P, vandenBelt M (1997) The value of the world’s ecosystem services and natural capital. Nature 387(6630):253–260CrossRefGoogle Scholar
  2. 2.
    Orth RJ, Carruthers TJB, Dennison WC, Duarte CM, Fourqurean JW, Heck KL, Hughes AR, Kendrick GA, Kenworthy WJ, Olyarnik S, Short FT, Waycott M, Williams SL (2006) A global crisis for seagrass ecosystems. Bioscience 56(12):987–996CrossRefGoogle Scholar
  3. 3.
    Short F, Carruthers T, Dennison W, Waycott M (2007) Global seagrass distribution and diversity: a bioregional model. J Exp Mar Bio Ecol 350(1–2):3–20CrossRefGoogle Scholar
  4. 4.
    Harrison PG, Bigley RE (1982) The recent introduction of the seagrass Zostera japonica Aschers and Graben to the pacific coast of North-America. Can J Fish Aquat Sci 39(12):1642–1648CrossRefGoogle Scholar
  5. 5.
    Young DR, Clinton PJ, Specht DT, DeWitt TH, Lee H (2008) Monitoring the expanding distribution of nonindigenous dwarf eelgrass Zostera japonica in a pacific northwest USA estuary using high resolution digital aerial orthophotography. J Spat Sci 53(1):87–97CrossRefGoogle Scholar
  6. 6.
    Baldwin JR, Lovvorn JR (1994) Expansion of seagrass habitat by the exotic Zostera japonica, and its use by dabbling ducks and brant in Boundary Bay, British-Columbia. Mar Ecol Prog Ser 103(1–2):119–127CrossRefGoogle Scholar
  7. 7.
    Abe M, Yokota K, Kurashima A, Maegawa M (2009) Temperature characteristics in seed germination and growth of Zostera japonica Ascherson & Graebner from Ago Bay, Mie Prefecture, central Japan. Fish Sci 75(4):921–927CrossRefGoogle Scholar
  8. 8.
    Hodoki Y, Ohbayashi K, Tanaka N, Kunii H (2013) Evaluation of genetic diversity in Zostera japonica (Aschers. et Graebn.) for seagrass conservation in brackish lower reaches of the Hii River System, Japan. Estuar coast 36(1):127–134CrossRefGoogle Scholar
  9. 9.
    Lee S, Ma S, Lim Y, Choi H-K, Shin H (2004) Genetic diversity and its implications in the conservation of endangered Zostera japonica in Korea. J Plant Biol 47(3):275–281CrossRefGoogle Scholar
  10. 10.
    Huang X, Huang L, Li Y, Xu Z, Fang J, Huang D, Han Q, Huang H, Tan Y, Liu S (2006) Main seagrass beds and threats to their habitats in the coastal sea of South China. Chin Sci Bull (S3), 114–119 (in Chinese) Google Scholar
  11. 11.
    Shafer DJ, Kaldy JE, Gaeckle JL (2014) Science and management of the introduced seagrass Zostera japonica in North America. Environ Manag 53(1):147–162CrossRefGoogle Scholar
  12. 12.
    Procaccini G, Olsen JL, Reusch TB (2007) Contribution of genetics and genomics to seagrass biology and conservation. J Exp Mar Biol Ecol 350(1):234–259CrossRefGoogle Scholar
  13. 13.
    Olsen JL, Stam WT, Coyer JA, Reusch TB, Billingham M, Boström C, Calvert E, Christie H, Granger S, Lumiere RL (2004) North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L. Mol Ecol 13(7):1923–1941CrossRefGoogle Scholar
  14. 14.
    Coyer JA, Diekmann OE, Serrao EA, Procaccini G, Milchakova N, Pearson GA, Stam WT, Olsen JL (2004) Population genetics of dwarf eelgrass Zostera noltii throughout its biogeographic range. Mar Ecol Prog Ser 281:51–62CrossRefGoogle Scholar
  15. 15.
    Arnaudhaond S, Migliaccio M, Diazalmela E, Teixeira S, De Vliet MSV, Alberto F, Procaccini G, Duarte CM, Serrao EA (2007) Vicariance patterns in the Mediterranean Sea: east–west cleavage and low dispersal in the endemic seagrass Posidonia oceanica. J Biogeogr 34(6):963–976CrossRefGoogle Scholar
  16. 16.
    Hernawan UE, van Dijk K-J, Kendrick GA, Feng M, Biffin E, Lavery PS, McMahon K (2017) Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo-Australian Archipelago. Mol Ecol 26(4):1008–1021CrossRefGoogle Scholar
  17. 17.
    Araki S, Kunii H (2006) Allozymic implications of the propagation of eelgrass Zostera japonica within a river system. Limnology 7(1):15–21CrossRefGoogle Scholar
  18. 18.
    Jiang K, Tsang P-KE, Xu N-N, Chen X-Y (2018) High genetic diversity and strong differentiation in dramatically fluctuating populations of Zostera japonica (Zosteraceae): implication for conservation. J Plant Ecol 11(5):789–797CrossRefGoogle Scholar
  19. 19.
    Jiang K, Gao H, Xu N-N, Tsang EPK, Chen X-Y (2011) A set of microsatellite primers for Zostera japonica (Zosteraceae). Am J Bot 98(9):e236–e238CrossRefGoogle Scholar
  20. 20.
    Zhang X, Zhou Y, Xue D, Liu J-X (2015) Development of microsatellite loci for the endangered seagrass Zostera japonica (Zosteraceae). Appl Plant Sci.  https://doi.org/10.3732/apps.1500064 Google Scholar
  21. 21.
    Zhang X, Zhou Y, Xue D-X, Liu J-X (2016) Genetic divergence of the endangered seagrass Zostera japonica Ascherson & Graebner between temperate and subtropical coasts of China based on partial sequences of matK and ITS. Biochem Syst Ecol 68:51–57CrossRefGoogle Scholar
  22. 22.
    Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2):193–208CrossRefGoogle Scholar
  23. 23.
    Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12(7):499–510CrossRefGoogle Scholar
  24. 24.
    Olsen JL, Rouze P, Verhelst B et al (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 530(7590):331–335CrossRefGoogle Scholar
  25. 25.
    Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18(2):233–234CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of OceanologyChinese Academy of SciencesQingdaoChina
  2. 2.Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
  3. 3.Center for Ocean Mega-ScienceChinese Academy of SciencesQingdaoChina

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