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Journal of Genetics

, Volume 97, Supplement 1, pp 79–86 | Cite as

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

  • Hao Song
  • Yi-xin Zhang
  • Mei-jie Yang
  • Jing-chun Sun
  • Tao Zhang
  • Hai-Yan Wang
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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.

Keywords

next-generation sequencing simple-sequence repeats gastropod Rapana venosa 

Notes

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.

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Copyright information

© Indian Academy of Sciences 2018

Authors and Affiliations

  1. 1.CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of OceanologyChinese Academy of SciencesQingdaoPeople’s Republic of China
  2. 2.Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoPeople’s Republic of China
  3. 3.University of Chinese Academy of SciencesBeijingPeople’s Republic of China
  4. 4.Center for Ocean Mega-ScienceChinease Academy of SciencesQingdoaPeople’s Republic of China
  5. 5.Qingdao No. 2 Middle School of Shandong ProvinceQingdaoPeople’s Republic of China

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