Skip to main content
SpringerLink
Log in

Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale

  • Online Resources
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

The veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with \({\sim }92\times \) sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2–28 and the observed heterozygosity was 0.2857–0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • An J., Yu H., Yu R., Kong L. and Li Q. 2013 Isolation and characterization of 23 microsatellite loci in the veined rapa whelk (Rapana venosa). Conserv. Genet. Resour. 5, 1049–1051.

    Article  Google Scholar 

  • Bolger A. M., Lohse M. and Usadel B. 2014 Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics  30, 2114–2120.

    Article  CAS  Google Scholar 

  • Chandler E. A., McDowell J. R. and Graves J. E. 2008 Genetically monomorphic invasive populations of the rapa whelk, Rapana venosa. Mol. Ecol.  17, 4079–4091.

    Article  CAS  Google Scholar 

  • Drapkin E. 1963 Effect of Rapana bezoar Linne (Mollusca, Muricidae) on the Black Sea fauna. Dokl. Akad. Nauk. SSSR 151, 700–703.

    Google Scholar 

  • Giberto D. A., Bremec C. S., Schejter L., Schiariti A., Mianzan H. and Acha E. M. 2006 The invasive rapa whelk Rapana venosa (Valenciennes 1846): status and potential ecological impacts in the Río de la Plata estuary, Argentina–Uruguay. J. Shellfish Res.  25, 919–924.

    Article  Google Scholar 

  • Gregory T. R. 2003 Genome size estimates for two important freshwater molluscs, the zebra mussel (Dreissena polymorpha) and the schistosomiasis vector snail (Biomphalaria glabrata). Genome  46, 841–844.

    Article  CAS  Google Scholar 

  • Hinegardner R. 1974 Cellular DNA content of the Mollusca. Comp. Biochem. Phys. A  47, 447–460.

    Article  CAS  Google Scholar 

  • Lanfranconi A., Hutton M., Brugnoli E. and Muniz P. 2009 New record of the alien mollusc Rapana venosa (Valenciennes 1846) in the Uruguayan coastal zone of Río de la Plata. Pan-Am. J. Aquat. Res.  4, 216–221.

    Google Scholar 

  • Li R., Yu C., Li Y., Lam T. W., Yiu S. M., Kristiansen K. et al. 2009 SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics  25, 1966–1967.

    Article  CAS  Google Scholar 

  • Li R., Zhu H., Ruan J., Qian W., Fang X., Shi Z. et al. 2010 De novo assembly of human genomes with massively parallel short read sequencing. Genome Res.  20, 265–272.

    Article  CAS  Google Scholar 

  • Liu J. X. and Avise J. C. 2011 High degree of multiple paternity in the viviparous Shiner perch, Cymatogaster aggregata, a fish with long-term female sperm storage. Mar. Biol.  158, 893–901.

    Article  Google Scholar 

  • Lowe A. J., Moule C., Trick M. and Edwards K. J. 2004 Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor. Appl. Genet.  108, 1103–1112.

    Article  CAS  Google Scholar 

  • Lu M., An H. and Li L. 2016 Genome survey sequencing for the characterization of the genetic background of Rosa roxburghii Tratt and leaf ascorbate metabolism genes. PLoS One  11, e0147530.

    Article  Google Scholar 

  • Luo R., Liu B., Xie Y., Li Z., Huang W., Yuan J. et al. 2012 SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience  1, 18.

    Article  Google Scholar 

  • Mann R., Harding J. M. and Westcott E. 2006 Occurrence of imposex and seasonal patterns of gametogenesis in the invading veined rapa whelk Rapana venosa from Chesapeake Bay, USA. Mar. Ecol. Prog. Ser.  310, 129–138.

    Article  Google Scholar 

  • Morgante M. and Olivieri A. M. 1993 PCR-amplified microsatellites as markers in plant genetics. Plant J.  3, 175.

    Article  CAS  Google Scholar 

  • Morgante M., Hanafey M. and Powell W. 2002 Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet.  30, 194–200.

    Article  CAS  Google Scholar 

  • Pascoe P. L., Jha A. N. and Dixon D. R. 2004 Variation of karyotype composition and genome size in some muricid gastropods from the northern hemisphere. J. Mollus. Stud.  70, 389–398.

    Article  Google Scholar 

  • Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S. et al. 1996 The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed.  2, 225–238.

    Article  CAS  Google Scholar 

  • R Core Team 2015 R: a language and environment for statistical computing. R foundation for statistical computing Vienna, Austria (http://www.R-project.org/).

  • Schell T., Feldmeyer B., Schmidt H., Greshake B., Tills O., Truebano M. et al. 2017 An annotated draft genome for Radix auricularia (Gastropoda, Mollusca). Genome Biol. Evol. 9, 585–592.

  • Sharma P. C., Grover A. and Kahl G. 2007 Mining microsatellites in eukaryotic genomes. Trends. Biotechnol.  25, 490–498.

    Article  CAS  Google Scholar 

  • Song H., Sun L.-Y., Yu Z.-L., Sun L.-N., Xue D.-X., Zhang T. et al. 2016a Metabolomic analysis of competent larvae and juvenile veined rapa whelks (Rapana venosa). Mar. Biol.  163, 1–8.

    Article  CAS  Google Scholar 

  • Song H., Wang H.-Y. and Zhang T. 2016b Comprehensive and quantitative proteomic analysis of metamorphosis-related proteins in the veined rapa whelk (Rapana venosa). Int. J. Mol. Sci.  17, 924.

    Article  Google Scholar 

  • Song H., Yu Z. L., Sun L. N., Gao Y., Zhang T. and Wang H. Y. 2016c De novo transcriptome sequencing and analysis of Rapana venosa from six different developmental stages using Hi-seq 2500. Comp. Biochem. Phys. D  17, 48–57.

    CAS  Google Scholar 

  • Song H., Yu Z. L., Sun L. N., Xue D. X., Zhang T. and Wang H. Y. 2016d Transcriptomic analysis of differentially expressed genes during larval development of Rapana venosa by digital gene expression profiling. G3 Genes Genom. Genet.  6, 2181–2193.

    CAS  Google Scholar 

  • Zhang H., Wei L., Miao H., Zhang T. and Wang C. 2012 Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics  13, 316.

    Article  CAS  Google Scholar 

  • Zhou W., Hu Y., Sui Z., Fu F., Wang J., Chang L. et al. 2013 Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing. PLoS One  8, e69909.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was supported by the National Natural Science Foundation of China (grant no. 31572636), the earmarked fund for Modern Agro-industry Technology Research System (CARS-49), the Primary Research and Development Plan of Shandong Province (grant no. 2016ZDJS06A02), the industry leading talents project of taishan scholars (recipient: Tao Zhang), the NSFC–Shandong Joint Fund for Marine Science Research Centers (grant no. U1606404), the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDA11020703) and the Creative Team Project of the Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology (no. LMEES-CTSP-2018-1). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Authors’ contributions

HS, TZ and HW conceived and designed the experiments. HS, JS and YZ performed the experiments. HS and MY analysed the data. TZ and HW contributed reagents, materials and analysis tools. HS wrote the paper.

Author information

Authors and Affiliations

  1. CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, People’s Republic of China

    Hao Song, Mei-jie Yang, Jing-chun Sun, Tao Zhang & Hai-Yan Wang

  2. Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People’s Republic of China

    Hao Song, Mei-jie Yang, Jing-chun Sun, Tao Zhang & Hai-Yan Wang

  3. University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China

    Hao Song & Mei-jie Yang

  4. Center for Ocean Mega-Science, Chinease Academy of Sciences, Qingdoa, 266071, People’s Republic of China

    Hao Song, Jing-chun Sun, Tao Zhang & Hai-Yan Wang

  5. Qingdao No. 2 Middle School of Shandong Province, Qingdao, 266071, People’s Republic of China

    Yi-xin Zhang

Authors
  1. Hao Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yi-xin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mei-jie Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jing-chun Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tao Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hai-Yan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Tao Zhang or Hai-Yan Wang.

Additional information

Corresponding editor: Silvia Garagna

HS, TZ and HW conceived and designed the experiments. HS, JS and YZ performed the experiments. HS and MY analysed the data. TZ and HW contributed reagents, materials and analysis tools. HS wrote the paper.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Song, H., Zhang, Yx., Yang, Mj. et al. Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale. J Genet 97 (Suppl 1), 79–86 (2018). https://doi.org/10.1007/s12041-018-0975-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12041-018-0975-z

Keywords

Search

Navigation