Skip to main content
SpringerLink
Log in

Development and characterization of SNP derived from spinyhead croaker (Collichthys lucidus) by RNA-seq

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

A novel set of SNP markers were detected from RNA-seq data of spinyhead croaker (Collichthys lucidus). Totally 49,617,970 clean reads and 78,671 putative SNPs were obtained. Among them, 40 SNPs were randomly selected to perform validation in 30 wild individuals of C. lucidus captured from 3 geographic stocks in the coast of China. Eventually, 29 SNP loci were successfully validated and showed bi-allelic polymorphism in genotyping by Sequenom MassARRAY. These novel SNPs provided useful genomic resources for C. lucidus, especially in population genetics, molecular assisted selection and conservation studies.

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

References

  • Gabriel S, Ziaugra L (2004) SNP genotyping using Sequenom MassARRAY 7 K Platform. Curr Protoc Hum Genet 42:1–16. doi:10.1002/0471142905.hg0212s42

    Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M et al (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 29:644–652. doi:10.1038/nbt.1883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo LL, Qiu YW, Zhang G et al (2008) Levels and bio-accumulation of organochlorine pesticides (OCPs) and polybrominated diphenyl ethers (PBDEs) in fishes from the Pearl River estuary and Daya Bay, South China. Environ Pollut 152:604–611. doi:10.1016/j.envpol.2007.06.067

    Article  CAS  PubMed  Google Scholar 

  • Helyar SJ, Hemmer HJ, Bekkevold D et al (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 11(Suppl 1):123–136. doi:10.1111/j.1755-0998.2010.02943.x

    Article  PubMed  Google Scholar 

  • Huang LM, Li J, Xie YJ et al (2010) Study of the Collichthys lucidus fisheries resources of the Minjiang Estuary and its adjacent waters. J Oceanogra Taiwan Strait 29:250–256

    Google Scholar 

  • Ma CY, Ma HY, Ma LB et al (2011) Development and characterization of 19 microsatellite markers for Collichthys lucidus. Conserv Genet Resour 3:503–506. doi:10.1007/s12686-011-9389-4

    Article  Google Scholar 

  • McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. doi:10.1101/gr.107524.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shawn JC, Paul FG, Victoria LS (2015) Evolutionary insights from denovo transcriptome assembly and SNP discovery in California white oaks Cokus et al. BMC Genomics 16:552. doi:10.1186/s12864-015-1761-4

    Article  Google Scholar 

  • Song N, Ma GQ, Zhang XM et al (2014) Genetic structure and historical demography of Collichthys lucidus inferred from mtDNA sequence analysis. Environ Biol Fish 97(1):69–77. doi:10.1007/s10641-013-0124-8

    Article  Google Scholar 

  • Song W, Jiang KJ, Zhang FY, Zhao M, Ma LB (2016) Molecular cloning and gene expression analysis of cystatin C-like proteins in spinyhead croaker Collichthys lucidus. Genet Mol Res 15(1). doi:10.4238/gmr.15017417

  • Thomas PD, Kejariwal A (2004) Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecllar effects. Proc Natl Acad Sci USA 101(43):15398–15403. doi:10.1073/pnas.0404380101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang PP, Xiao SJ, Han ZF et al (2015) SNP discovery in large yellow croaker (Larimichthys crocea) using Roche 454 pyrosequencing sequencing platform. Conserv Genet Resour 7(4):777–779. doi:10.1007/s12686-015-0481-z

    Article  Google Scholar 

  • Yeh FC, Yang R, Boyle TJ et al (2000) POPGENE 32, microsoft windows-based freeware for popllation genetic analysis: molecllar biology and biotechnology centre. University of Alberta, Edmonton

    Google Scholar 

  • Zheng DF, Zhao JL, Zhou WY et al (2011) Genetic structure of Collichthys lucidus populations from China coastal areas by AFLP analysis. Oceanologia et Limnologia Sinica 42(3):443–447

    Google Scholar 

Download references

Acknowledgements

This work was supported by the Basic Research Fund for State-Level Nonprofit Research Institutes of ESCFRI, CAFS(#Dong2015M08) and the National Infrastructure of Fishery Germplasm Resources.

Author information

Authors and Affiliations

  1. Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China

    Wei Chen, Wei Song, Fenfang Chen, Ming Zhao, Chunyan Ma, Fengying Zhang, Wei Wang & Lingbo Ma

  2. College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China

    Fenfang Chen

Authors
  1. Wei Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wei Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fenfang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ming Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chunyan Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Fengying Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Lingbo Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Wei Song or Lingbo Ma.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, W., Song, W., Chen, F. et al. Development and characterization of SNP derived from spinyhead croaker (Collichthys lucidus) by RNA-seq. Conservation Genet Resour 9, 573–577 (2017). https://doi.org/10.1007/s12686-017-0725-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-017-0725-1

Keywords

Search

Navigation