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Analysis on Microsatellite Loci of Daphnia similoides sinensis and Rapid Development of Primer Based on Transcriptome Sequencing

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Abstract

In this study, we performed transcriptome sequencing of D. similoides sinensis and developing of simple sequence repeats (SSRs) markers to identify valuable markers for Daphnia molecular genetics. The total length of D. similoides sinensis transcriptome sequence was 40 093 546 bp, which contained 12 017 SSR markers and 21 344 microsatellite loci. 2164 SSR primer pairs were obtained through design for 21 344 sequences which contained the loci of SSRs. 60 primer pairs were randomly selected, 11 SSR primer pairs with polymorphism were obtained by polyacrylamide gel electrophoresis and capillary electrophoresis. A total of 88 alleles of SSRs were amplified, of which 52 belonged to polymorphic loci (the percentage of polymorphic loci was 59%). The polymorphism information content of the 11-pairs SSR primers ranged from 0.4 to 0.75, with an average of 0.58, indicating that these primers had rich polymorphism. The results suggested that the 11 primers pairs might provide important values in revealing the genetic diversity and phyletic evolution of D. similoides sinensis.

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REFERENCES

  1. Hebert, P.H.D., The population biology of Daphnia (Crustacea, Daphnidae), Biol. Rev., 1978, vol. 53, no. 3, pp. 387—426. https://doi.org/10.1111/j.1469-185X.1978.tb00860.x

    Article  Google Scholar 

  2. Lampert, W., Daphnia: Development of Model Organism in Ecology and Evolution. American Institute of Biological Sciences, Washington DC. Identification of the microinvertebrates of the continental waters of the world, Q. Rev. Biol., 2011, vol. 80, pp. 491—510.

    Google Scholar 

  3. Puerari, R.C., Costa, C.H., Vicentini, D.S., et al., Synthesis, characterization and toxicological evaluation of Cr2O3 nanoparticles using Daphnia magna and Aliivibrio fischeri, Ecotox. Environ. Safe, 2016, vol. 128, pp. 36—43. https://doi.org/10.1016/j.ecoenv.2016.02.011

    Article  CAS  Google Scholar 

  4. Xu, M., Zhang, H.J., Deng, D.G., et al., Phylogenetic relationship and taxonomic status of four Daphnia species based on 16S rDNA and COI sequence, Acta Hydrobiol. Sin., 2014, vol. 38, no. 6, pp. 1040—1046. https://doi.org/10.7541/2014.153

    Article  CAS  Google Scholar 

  5. Griebel, J., Gießler, S., Yin, M., et al., Parental and hybrid Daphnia from the D. longispina complex: long-term dynamics in genetic structure and significance of overwintering modes, J. Genet., 2016, vol. 29, no. 4, pp. 810—823. https://doi.org/10.1111/jeb.12828

    Article  CAS  Google Scholar 

  6. Benzie, J.A.H., The Genus Daphnia (Including Daphniopsis) (Anomopoda: Daphniidae), Leiden, 2005.

  7. Jiang, X.Z. and Du, N.S., Fauna Sinica: Crustacean, Freshwater Cladocera, Science Press, 1979.

    Google Scholar 

  8. Gu, Y.L., Xu, L., Lin, Q.Q., et al., A new subspecies of Daphnia: Daphnia similoides sinensis, Ecol. Sci., 2013, vol. 32, no. 3, pp. 308—312. https://doi.org/10.3969/j.issn.1008-8873.2013.03.008

    Article  Google Scholar 

  9. Popova, E.V., Petrusek, A., Kořínek, V., et al., Revision of the Old World Daphnia (Ctenodaphnia) similis group (Cladocera: Daphniidae), Zootaxa, 2016, vol. 4161, no. 1, pp. 001—040. https://doi.org/10.11646/zootaxa.4161.1.1

  10. Wang, W.P., Zhang, K., Deng, D.G., et al., Genetic diversity of Daphnia pulex in the middle and lower reaches of the Yangtze River, PLoS One, 2016, vol. 11, no. 3. e0152436. https://doi.org/10.1371/journal.pone.0152436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Bi, Y.H., Wu, Y.Y., and Zhou, Z.G., Genetic diversity of wild population of Pyropia haitanensis based on SSR analysis, Biochem. Syst. Ecol., 2014, vol. 54, no. 2, pp. 307—312. https://doi.org/10.1016/j.bse.2014.02.010

  12. Zeinalabedini, M., Dezhampour, J., Majidian, P., et al., Molecular variability and genetic relationship and structure of Iranian Prunus rootstocks revealed by SSR and AFLP markers, Sci. Hortic. (Amsterdam), 2014, vol. 172, no. 3, pp. 258—264. https://doi.org/10.1016/j.scienta.2014.04.006

    Article  CAS  Google Scholar 

  13. Kardpal, R.P., Kandpal, G., and Weissman, S.M., Construction of libraries enrich for sequence repeats and jumping clones, and hybridization selection for region-specific markers, Proc. Natl. Acad. Sci. U.S.A., 1994, vol. 91, no. 1, pp. 88—92. https://doi.org/10.1073/pnas.91.1.88

    Article  Google Scholar 

  14. Edwards, K., Barker, J., Darly, A., et al., Microsatellite libraries enrich for several microsatellite sequences in plants, Biotechniques, 1996, vol. 20, no. 5, pp. 758—760.

    Article  CAS  PubMed  Google Scholar 

  15. Cheng, X.F., Huang, F.J., Liu, M.D., et al., Development of microsatellite markers using 454 pyrosequencing, Biotechnol. Bull., 2011, vol. 8, pp. 84—90. https://doi.org/10.13560/j.cnki.Biotech.Bull.1985.2011.08.032

  16. Parragonzález, L.B., Aravenaabarzúa, G.A., Navarronavarro, C.S., et al., Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies, BMC Genomics, 2012, vol. 13, no. 1, pp. 1—15. https://doi.org/10.1186/1471-2164-13-425

  17. Shendure, J. and Ji, H., Next-generation DNA sequencing, Nat. Biotechnol., 2008, vol. 26, no. 10, pp. 1135—1145. https://doi.org/10.1038/nbt1486

    Article  CAS  PubMed  Google Scholar 

  18. Karagyozov, L., Kalcheva, I.D., and Chapman, V., Construction of random small-insert genomic libraries highly enriched for simple sequence repeats, Nucleic Acids Res., 1993, vol. 21, no. 16, pp. 3911—3912. https://doi.org/10.1093/nar/21.16.3911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ren, G.J., Development of microsatellite DNA markers and population genetics for sand lance (Ammodytes personatus) and roughskin sculpin (Trachidermus fasciatus), Ph.D. thesis, Ocean University of China, 2012.

  20. Yue, G.H., Ho, M.Y., Orban, L., et al., Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp, Aquaculture, 2004, vol. 234, no. 1, pp. 85—98. https://doi.org/10.1016/j.aquaculture.2003.12.021

    Article  CAS  Google Scholar 

  21. Srikwan, S., Hufford, K., Eggert, L., et al., Variable microsatellite markers for genotyping tree shrews, Tupaia, and their potential use in genetic studies of fragmented populations, Scienceasia, 2002, vol. 28, pp. 93—97. https://doi.org/10.2306/scienceasia1513-1874.2002.28.093

    Article  Google Scholar 

  22. Ma, Z.Q., Röder, M., and Sorrells, M.E., Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat, Genome, 1996, vol. 39, no. 1, pp. 123—130. https://doi.org/10.1139/g96-017

    Article  CAS  PubMed  Google Scholar 

  23. Zeng, C., Gao, Z.X., Luo, W., et al., Characteristics of microsatellites in blunt snout bream (Megalobrama amblycephala) EST sequences using 454 flx, Acta Oceanol. Sin., 2013, vol. 37, no. 5, pp. 982—988. https://doi.org/10.7541/2013.129

    Article  CAS  Google Scholar 

  24. Toth, G., Gaspari, Z., and Jurka, J., Microsatellites in different eukaryotic genomes: survey and analysis, Genome Res., 2000, vol. 10, no. 7, pp. 967—981. https://doi.org/10.1101/gr.10.7.967

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Peng, W., Bao, Z.M., Du, H.X., et al., Development and characterization of 38 novel EST-SSRs for the sea cucumber Apostichopus japonicas, Conserv. Genet. Res., 2009, vol. 1, no. 1, pp. 447—450. https://doi.org/10.1007/s12686-009-9103-y

    Article  Google Scholar 

  26. Botstein, D., White, R.L., Skolnick, M., et al., Construction of a genetic linkage map in man using restriction fragment length polymorphism, Am. J. Hum. Genet., 1980, vol. 32, no. 3, pp. 314—331.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Cordeiro, G.M., Casu, R., McIntyre, C.L., et al., Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and Sorghum, Plant Sci., 2001, vol. 160, no. 16, pp, 1115—1123. https://doi.org/10.1016/S0168-9452(01)00365-X

  28. Hu, J., Nakatani, M., Mizuno, K., et al., Development and characterization of microsatellite markers in sweet potato, Breed. Sci., 2004, vol. 54, no. 2, pp. 177—188. https://doi.org/10.1270/jsbbs.54.177

    Article  CAS  Google Scholar 

  29. Dong, Y., Han, J., and Cai, H.C., Cross-species amplification and characterization of polymorphic microsatellite loci in Hong Kong grouper, Epinephelus akaara, J. Beijing Norm. Univ. (Nat. Sci.), 2008, vol. 44, no. 5, pp. 511—514. https://doi.org/10.3321/j.issn:0476-0301.2008.05.016

    Article  CAS  Google Scholar 

  30. Russell, J., Boorh, A., Fuller, J., et al., Comparison of sequence base on polymorphism and haplotype content in transcribed and anonymous regions of the barley, Genome, 2004, vol. 47, no. 2, pp. 389—398. https://doi.org/10.1139/G03-125

    Article  CAS  PubMed  Google Scholar 

  31. Scott, K.D., Eggler, P., Seaton, G., et al., Analysis of SSRs derived from grape ESTs, Theor. Appl. Genet., 2000, vol. 100, no. 5, pp. 723—726. https://doi.org/10.1007/s001220051344

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Funding

This work was supported by grants from the National Natural Science Foundation of China (no. 31370470).

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Authors and Affiliations

  1. School of Resource and Environmental Engineering, Anhui University, 230601, Hefei, China

    J. X. Wu, X. X. Xu & Z. Z. Zhou

  2. Anhui Key Laboratory of Resource and Plant Biology, School of Life Science, Huaibei Normal University, 235000, Huaibei, P.R. China

    J. X. Wu, Y.-N. Zhang, D. D. Deng & X. X. Xu

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  1. J. X. Wu
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  2. Y.-N. Zhang
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  3. D. D. Deng
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  4. X. X. Xu
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Correspondence to D. D. Deng or Z. Z. Zhou.

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Wu, J.X., Zhang, YN., Deng, D.D. et al. Analysis on Microsatellite Loci of Daphnia similoides sinensis and Rapid Development of Primer Based on Transcriptome Sequencing. Russ J Genet 55, 711–719 (2019). https://doi.org/10.1134/S1022795419060188

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