Skip to main content
SpringerLink
Log in

Isolation and characterization of genic microsatellites from de novo assembly transcriptome in the bivalve Ruditapes philippinarum

  • Biology
  • Published:
Journal of Oceanology and Limnology Aims and scope Submit manuscript

Abstract

The marine bivalve Ruditapes philippinarum (Veneridae) has always been an economically important aquaculture species. In this study, 106 831 unigenes and 2 664 SSR loci (1 locus/40 sequences) were achieved from the de novo assembly transcriptome. Among all the SSRs, tri-nucleotides (46.40%) was the most, followed by di-nucleotides (32.43%). Meanwhile, AAC/GTT (19.82%) was the most common SSR loci searched. After polymorphism detection using 32 wild R. philippinarum individuals, 34 polymorphic and 3 monomorphic SSR loci were screened, and the genetic index of them was calculated. The results show that PIC of 30 polymorphic SSR loci was at medium and high levels (PIC>0.25). However, there were five SSR polymorphic loci (e.g. MG871423, MG871428, MG871429, MG871434, MG871435) deviating from the Hardy-Weinberg equilibrium after the Bonferroni correction (adjusted P=0.001 471). The Na value (number of alleles per locus) ranged from 2 to 7. In addition, the Ho (observed heterozygosities) and He (expected heterozygosities) were 0.100 0–1.000 0 and 0.191 3–0.723 6, respectively. Therefore, RNA-Seq was shown as a fast and cost-effective method for genic SSR development in non-model species. Meanwhile, the 37 loci from R. philippinarum will further enrich the genetic information and advance the population conservation and restoration.

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

Similar content being viewed by others

References

  • Bai Z Y, Zheng H F, Lin J Y, Wang G L, Li J L. 2013. Comparative analysis of the transcriptome in tissues secreting purple and white nacre in the pearl mussel Hyriopsis cumingii. PLoS One, 8(1): e53617.

    Article  Google Scholar 

  • Bouck A, Vision T. 2007. The molecular ecologist’s guide to expressed sequence tags. Molecular Ecology, 16(5): 907–924.

    Article  Google Scholar 

  • Chistiakov D A, Hellemans B, Volckaert F A M. 2006. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture, 255(1–4): 1–29.

    Article  Google Scholar 

  • Cong M, Wu H F, Cao T F, Lü J S, Wang Q, Ji C L, Li C H, Zhao J M. 2018. Digital gene expression analysis in the gills of Ruditapes philippinarum, exposed to short- and long-term exposures of ammonia nitrogen. Aquatic Toxicology, 194: 121–131.

    Article  Google Scholar 

  • Ellis J R, Burke J M. 2007. EST-SSRs as a resource for population genetic analyses. Heredity, 99(2): 125–132.

    Article  Google Scholar 

  • FAO (Food and Agriculture Organization). 2014. Fishery and Aquaculture Statistics 2010. Food and Agriculture Organization of the United Nations, Rome.

    Google Scholar 

  • Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q D, Chen Z H, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7): 644–652.

    Article  Google Scholar 

  • Hégaret H, da Silva P M, Wikfors G H, Lambert C, De Bettignies T, Shumway S E, Soudant P. 2007. Hemocyte responses of Manila clams, Ruditapes philippinarum, with varying parasite, Perkinsus olseni, severity to toxicalgal exposures. Aquatic Toxicology, 84(4): 469–479.

    Article  Google Scholar 

  • Jiang Q, Li Q, Yu H, Kong L F. 2014. Genome-wide analysis of simple sequence repeats in marine animals-a comparative approach. Marine Biotechnology, 16(5): 604–619.

    Article  Google Scholar 

  • Kong L F, Bai J, Li Q. 2014. Comparative assessment of genomic SSR, EST-SSR and EST-SNP markers for evaluation of the genetic diversity of wild and cultured Pacific oyster, Crassostrea gigas Thunberg. Aquaculture, 420–421: S85–S91.

    Article  Google Scholar 

  • Li J T, Li J, Chen P, Liu P, He Y Y. 2015. Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, annotation and marker discovery. Molecular Biology Reports, 42(1): 135–147.

    Article  Google Scholar 

  • Lü Z M, Hou L, Gong L, Liu L Q, Chen Y J, Guo B Y, Dong Y H, Wu C W. 2017. Isolation and analysis on EST microsatellites of Sepiella japonica by de novo high-throughput transcriptome sequencing. Oceanologia et Limnologia Sinica, 48(4): 877–883. (in Chinese with English abstract)

    Google Scholar 

  • Mandal S, Jena J K, Singh R K, Mohindra V, Lakra W S, Deshmukhe G, Pathak A, Lal K K. 2016. De novo development and characterization of polymorphic microsatellite markers in a schilbid catfish, Silonia silondia (Hamilton, 1822) and their validation for population genetic studies. Molecular Biology Reports, 43(2): 91–98.

    Article  Google Scholar 

  • Marshall T C, Slate J, Kruuk L E, Pemberton J M. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7(5): 639–655.

    Article  Google Scholar 

  • Nie H T, Niu H B, Zhao L Q, Yang F, Yan X W, Zhang G F. 2015. Genetic diversity and structure of Manila clam (Ruditapes philippinarum) populations from Liaodong peninsula revealed by SSR markers. Biochemical Systematics and Ecology, 59: 116–125.

    Article  Google Scholar 

  • Nie H T, Zhu D P, Yang F, Zhao L Q, Yan X W. 2014. Development and characterization of EST-derived microsatellite makers for Manila clam (Ruditapes philippinarum). Conservation Genetics Resources, 6(1): 25–27.

    Article  Google Scholar 

  • Parchman T L, Geist K S, Grahnen J A, Benkman C W, Buerkle C A. 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11: 180.

    Article  Google Scholar 

  • Qiu L J, Yang C, Tian B, Yang J B, Liu A Z. 2010. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biology, 10: 278.

    Article  Google Scholar 

  • Schorderet D F, Gartler S M. 1992. Analysis of CpG suppression in methylated and nonmethylated species. Proceedings of the National Academy of Sciences of the United States of America, 89(3): 957–961.

    Article  Google Scholar 

  • Sun X J, Li D M, Liu Z H, Zhou L Q, Wu B, Yang A G. 2017. De novo assembly of pen shell (Atrina pectinata) transcriptome and screening of its genic microsatellites. Journal of Ocean University of China, 16(5): 882–888.

    Article  Google Scholar 

  • van Oosterhout C, Hutchinson W F, Wills D P M, Shipley P. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4(3): 535–538.

    Article  Google Scholar 

  • Varshney R K, Graner A, Sorrells M E. 2005b. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology, 23(1): 48–55.

    Article  Google Scholar 

  • Varshney R K, Sigmund R, Börner A, Korzun V, Stein N, Sorrells M E, Langridged P, Granera A. 2005a. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science, 168(1): 195–202.

    Article  Google Scholar 

  • Wen Y F, Uchiyama K, Han W J, Ueno S, Xie W D, Xu G B, Tsumura Y. 2013. Null alleles in microsatellite markers. Biodiversity Science, 21(1): 117–126. (in Chinese with English abstract)

    Article  Google Scholar 

  • Wu H F, Liu X L, Zhao J M, Yu J B. 2011. NMR-based metabolomic investigations on the differential responses in adductor muscles from two pedigrees of Manila clam Ruditapes philippinarum to cadmium and zinc. Marine Drugs, 9(9): 1566–1579.

    Article  Google Scholar 

  • Yamini K N, Ramesh K, Naresh V, Rajendrakumar P, Anjani K, Kumar V D. 2013. Development of EST SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.). Journal of Plant Biochemistry and Biotechnology, 22(1): 90–102.

    Article  Google Scholar 

  • Yan L L, Qin Y J, Yan X W, Wang L N, Bi C L, Zhang J Y. 2015. Development of microsatellite markers in Ruditapes philippinarum using next-generation sequencing. Acta Ecologica Sinica, 35(5): 1573–1580. (in Chinese with English abstract)

    Google Scholar 

  • Yasuda N, Nagai S, Yamaguchi S, Lian C L, Hamaguchi M. 2007. Development of microsatellite markers for the Manila clam Ruditapes philippinarum. Molecular Ecology Notes, 7(1): 43–45.

    Article  Google Scholar 

  • Yeh F C, Yang R, Boyle T J, Ye Z, Xiyan J M. 2000. PopGene 32, Microsoft Window-based freeware for population Genetic Analysis. Version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Canada.

    Google Scholar 

  • Zhu D P, Nie H T, Qin Y J, Li J, Liu L H, Yan X W. 2015. Development and characterization of 38 microsatellite makers for Manila clam (Ruditapes philippinarum). Conservation Genetics Resources, 7(2): 517–520.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Xiamen, 361021, China

    Jingbo Shangguan, Anle Xu, Xiaowei Hu & Zhongbao Li

  2. Fisheries College, Jimei University, Xiamen, 361021, China

    Jingbo Shangguan, Anle Xu, Xiaowei Hu & Zhongbao Li

Authors
  1. Jingbo Shangguan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anle Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiaowei Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhongbao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhongbao Li.

Additional information

Supported by the National Natural Science Foundation of China (No. 31272668) and the Natural Science Foundation of Fujian Province (No. 2017J01638)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shangguan, J., Xu, A., Hu, X. et al. Isolation and characterization of genic microsatellites from de novo assembly transcriptome in the bivalve Ruditapes philippinarum. J. Ocean. Limnol. 37, 1071–1079 (2019). https://doi.org/10.1007/s00343-019-8071-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00343-019-8071-7

Keyword

Search

Navigation