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

  • Jingbo Shangguan
  • Anle Xu
  • Xiaowei Hu
  • Zhongbao LiEmail author


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.


Ruditapes philippinarum transcriptome microsatellite genetic diversity 


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Copyright information

© Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Jingbo Shangguan
    • 1
    • 2
  • Anle Xu
    • 1
    • 2
  • Xiaowei Hu
    • 1
    • 2
  • Zhongbao Li
    • 1
    • 2
    Email author
  1. 1.Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-EnvironmentXiamenChina
  2. 2.Fisheries CollegeJimei UniversityXiamenChina

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