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Development of Genetic Novel SSR Markers by Transcriptome Sequencing in Ophicephalus argus Cantor

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Abstract

Northern snakehead Ophiocephalus argus Cantor is an endemic freshwater species in China. This species is widely distributed in the lower Yellow and Yangtze river systems in eastern China. In the present study, six cDNA libraries of Ophiocephalus argus were sequenced using Illumina HiSeq4000 paired-end sequencing technology. 67 564 sequences from 79 500 964 paired-end reads were generated. A total of 7182 unigenes were clustered into 25 functional categories by searching against the COG database, and BLAST2GO search assigned 33 710 unigenes to 59 GO terms. From the 67 564 assembled unique sequences, 21 464 SSRs were identified in 14 997 unique sequences. Among the 7992 with compound formation (SSRs), 100 primer pairs were successfully designed for further validation, and 42 of them produced polymorphic products in Ophiocephalus argus individuals. The number of alleles per locus ranged from 5 to 19, the observed and expected heterozygosity estimates ranged from 0.178 to 0.985 and from 0.421 to 0.929, respectively. The generation of such larges cale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development.

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REFERENCES

  1. Jabeen, M. and Afzal, M., Densitometric analysis of serum transferrins in two air-breathing fish (Channidae: Channiformes), Asian J. Biochem., 2010, vol. 5, no. 4, pp. 214—221.

    Article  Google Scholar 

  2. Xiao, M. S., Cui, F., Kang, J., and Zhang, X.H., Genetic structure and variation of wild Ophicephalus argus Cantor from Huaihe River based on mtDNA D-loop sequences. J. Huazhong Nor. Univ.(Nat. Sci.), 2013, vol. 47, no. 1, pp. 82—90 (in Chinese).

    CAS  Google Scholar 

  3. Wu, X.W., Economy Fauna of China, Beijing: Science Press, 1979.

    Google Scholar 

  4. Liu, J., Cui, Y., and Liu, J., Resting metabolism and heat increment of feeding in mandarin fish (Siniperca chuatsi) and Chinese snakehead (Channa argus), Comp. Biochem. Physiol., Part A: Mol. Integr. Physiol., 2000, vol. 127, pp. 131—138.

    Article  CAS  Google Scholar 

  5. Lou, L., A test on the culture of Channa argus, Freshwater Fish.,1995, no. 5, pp. 38—40 (in Chinese).

  6. Wu, L. F., Zhang, D. M., Huang, Q., and Liu, C.L., The food analysis, population resources and utilization of snakehead fish (Ophiocephelus argus) in Huanghua Lake, J. Jilin Agric. Univ., 2000, vol. 22, no. 3, pp. 104—106 (in Chinese).

    Google Scholar 

  7. Yu, H.Y., Ou, Y.S., Wu, X.P., Dai, Y.G., and Zou, S.Y., Studies on age and growth of Ophiocephalus argus in Poyang Lake, Life Sci. Res., 2008, vol. 12, no. 1, pp. 91—94 (in Chinese).

    Google Scholar 

  8. Landis, G.A.M., Lapointe, N.W.R., and Angermeier, P.L., Individual growth and reproductive behavior in a newly established population of northern snakehead (Channa argus), Potomac River, U.S.A., Hydrobiologia, 2011, vol. 661, pp. 123—131.

    Article  Google Scholar 

  9. Li, J.W., Biological characteristics and artificial culture techniques of Ophiocephalus argus, China Fish., 1999, no. 10, pp. 28—31.

  10. Huang, Z.P., The culture technique of Channa argus in pond, J. Aquacult., 2011, no. 2, pp. 37—38 (in Chinese).

  11. Zhang, X.Q., Gong, S.Y., Liu, J., He, X.G., and Gao, J.H., Studies on age and growth of Channa argus in the Wanghu Lake, Acta Hydrobiol. Sin., 1999, vol. 23, no. 6, pp. 600—603.

    Google Scholar 

  12. Nie, G.X., Fu, Y.R., Zhang, H., and Wei, X.J., The analysis of nutrition components in the muscle of Channa argus,Freshwater Fish., 2002, vol. 32, no. 2, pp. 46—47 (in Chinese).

    Google Scholar 

  13. Qin, W., Ni, J.G., Zhang, X.B., and Zhou, J.F., Comparative studies on chromosomes in the snakehead fish Channa argus and Ophiocephalidae,Reservoir Fish., 2004, vol. 24, no. 5, pp. 14—16 (in Chinese).

    Google Scholar 

  14. Yin, W.L. and Dai, J.H., Studies on the isozymes of different tissues in Ophiocephalus argus, J. Huazhong Nor. Univ.(Nat. Sci.), 2000, vol. 20, no. 3, pp. 17—20 (in Chinese).

    Google Scholar 

  15. Li, X., Ou, Y.S., Wu, X.P., Dai, Y.G., Hua, Y.Q., and Jiao, L., Studies on the EST and LDH isozymes in different tissues of Ophicephalus argus in Poyang Lake, HubeiAgric. Sci., 2010, vol. 49, no. 1, pp. 153—155.

    Google Scholar 

  16. Zhuo, X.L., Liang, R.S., Chen, Y.F., Huang, G.J., Yu, D.H., and Zou, J.X., Genetic characterization of northern snakehead (Channa argus) populations in China using microsatellite markers, Biochem. Syst. Ecol., 2012, vol. 43, pp. 25—31.

    Article  CAS  Google Scholar 

  17. Li, D.Y., Kang, D.H., Yin, Q.Q., Sun, X.W., and Liang, L.Q., Microsatellite DNA marker analysis of genetic diversity in wild common carp (Cyprinus carpio L.) populations, J. Genet. Genomics, 2007, vol. 34, no. 11, pp. 984—993.

    Article  CAS  Google Scholar 

  18. Xiao, M.X., Xia, H., and Bao, F., Isolation and characterization of 15 microsatellite loci for Ophicephalus argus Cantor, Russ. J. Genet., 2015, vol. 51, no. 10, pp. 1044—1047.

    Article  CAS  Google Scholar 

  19. Li, H.J., Liu, M., Ye, S., and Yang, F., De novo assembly, gene annotation, and molecular marker development using Illumina paired-end transcriptome sequencing in the clam Saxidomus purpuratus,Genes Genom., 2017, vol. 39, no. 6, pp. 675—685.

    Article  CAS  Google Scholar 

  20. Núñez-Acuña, G. and Gallardo-Escárate, C., Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing, Fish Shellfish Immun., 2013, vol. 35, pp. 1899—1905.

    Article  Google Scholar 

  21. Li, H.J., Zhang, J.J., Li, H.B., Gao, X.G., and He, C.B., Development and characterization of 13 polymorphic microsatellite markers for the Chinese surf clam (Mactra chinensis) through Illumina pairedend sequencing, Conserv. Genet. Resour., 2014, no. 6, pp. 877—879.

  22. Grabherr, M. G., Haas, B. J., Yassour, M., et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol., 2011, vol. 29, no. 7, pp. 644—652.

    Article  CAS  Google Scholar 

  23. Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., and Jensen, L.J., STRING v9.1: protein—protein interaction networks, with increased coverage and integration, Nucleic Acids Res., 2013, vol. 41, pp. D808—D815.

    Article  CAS  Google Scholar 

  24. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L., BLAST+: architecture and applications, BMC Bioinf., 2009, no. 10, p. 421.

    Article  Google Scholar 

  25. Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., and Robles, M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 2005, vol. 21, pp. 3674—3676.

    Article  CAS  Google Scholar 

  26. Thiel, T., Michalek, W., Varshney, R.K., and Graner, A.A., Exploiting EST databases for the development and characterization of gene derived SSR-markers in barley (Hordeum vulgare L.), Theor. Appl. Genet., 2003, no. 10, pp. 411—422.

  27. Bassam, B.J., Caetano-Anolles, G., and Gresshoff, P.M., Fast and sensitive silver staining of DNA in polyacrylamide gels, Anal. Biochem., 1991, vol. 196, pp. 80—83.

    Article  CAS  Google Scholar 

  28. Rousset, F., Genepop’007: a complete re-implementation of the Genepop software for Windows and Linux, Mol. Ecol. Resour., 2008, no. 8, pp. 103—106.

    Article  Google Scholar 

  29. Yeh, F.C. and Yang, R.C., POPGENE version 1.31, Microsoft Window-Based Freeware for Population Genetic Analysis, Edmonton: University of Alberta, 1999. http://microsoft.com/softlib/ slfiles/hpgl.exe.

    Google Scholar 

  30. Xu, P., Zhang, X.F., Wang, X.M., Li, J.T., Liu, G.M., Kuang, Y.Y., et al., Genome sequence and genetic diversity of the common carp, Cyprinus carpio,Nat. Genet., 2014, vol. 46, pp. 1212—1219.

    Article  CAS  Google Scholar 

  31. Howe, K., Clark, M.D., Torroja, C.F., et al., The zebrafish reference genome sequence and its relationship to the human genome, Nature, 2013, vol. 496, pp. 498—503.

    Article  CAS  Google Scholar 

  32. Li, D.J., Deng, Z., Qin, B., Liu, X.H., and Men, Z.H., De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.), BMC Genomics, 2012, no. 13, pp. 192—206.

  33. Ma, K., Qiu, G., Feng, J., and Li, J., Transcriptome analysis of the oriental river prawn, Macrobrachium nipponense using 454 pyrosequencing for discovery of genes and markers, PLoS One, 2012, vol. 7, no. 6. e39727

    Article  CAS  Google Scholar 

  34. Liao, X., Cheng, L., Xu, P., Lu, G., Wachholtz, M., Sun, X.W., and Chen, S.L., Transcriptome analysis of Crucian Carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species, PLoS One, 2013, vol. 8, no. 4. e62308

    Article  CAS  Google Scholar 

  35. Li, Y.H., Wang, H.P., Yao, H., O’Bryant, P., Rapp, D., Guo, L., and Waly, E.A., De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens,PLoS One, 2017, vol. 12, no. 2. e0171187

    Article  Google Scholar 

  36. Wang, L.H., Zhang, Y.X., Qi, X.Q., Gao,Y., and Zhang, X.R., Development and characterization of 59 polymorphic cDNA-SSR markers for the edible oil crop Sesamum indiwcum (Pedaliaceae), Am. J. Bot., 2012, no. 10, pp. e394—e398. http://www.amjbot.org/content/99/10/e394.full-aff-1.

    Article  Google Scholar 

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ACKNOWLEDGMENTS

We would like to thank the anonymous reviewers for the helpful comments. This research was supported by the Natural Science Foundation of Anhui Province, China (1708085MC78), Anhui Province Aquaculture Industry Technology System (Sciences and Technology education department, Anhui Provincial Agriculture Commission, China (2016 [84]), Anhui Province Key Research and Development Plan Project, China (1804a070200119).

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Authors and Affiliations

  1. College of Life and Health Science, Anhui Science and Technology University, 233100, Fengyang, Anhui, China

    M. Xiao, F. Bao & Y. Zhao

  2. Fisheries Research Institute, Anhui Academy of Agricultural Sciences, 230031, Hefei, Anhui, China

    J. He

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  1. M. Xiao
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Correspondence to J. He.

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Conflict of interest. Mingsong Xiao, Fangyin Bao, Yan Zhaoand Jixiang He declare that they have no conflict of interests.

Statement on the welfare of animals. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

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Xiao, M., Bao, F., Zhao, Y. et al. Development of Genetic Novel SSR Markers by Transcriptome Sequencing in Ophicephalus argus Cantor. Russ J Genet 56, 253–260 (2020). https://doi.org/10.1134/S1022795420020143

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