Isolation and characterization of genic microsatellites from de novo assembly transcriptome in the bivalve Ruditapes philippinarum
- 5 Downloads
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.
KeywordRuditapes philippinarum transcriptome microsatellite genetic diversity
Unable to display preview. Download preview PDF.
- Bouck A, Vision T. 2007. The molecular ecologist’s guide to expressed sequence tags. Molecular Ecology, 16(5): 907–924.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.CrossRefGoogle 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 highthroughput 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.CrossRefGoogle 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): 1 573–1 580.(in Chinese with English abstract)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