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De novo assembly of pen shell (Atrina pectinata) transcriptome and screening of its genic microsatellites

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Abstract

The pen shell (Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes (18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats (SSRs) were identified, of them the most abundant type was mono-nucleotide repeats (12902, 55.01%), which was followed by di-nucleotide (8132, 34.68%), tri-nucleotide (2010, 8.57%), tetra-nucleotide (401, 1.71%), and penta-nucleotide (7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.

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References

  • An, H. S., Kim, B. H., Lee, J. W., Dong, C. M., Kim, S. K., and Yi, C. K., 2011. Comparison between wild and hatchery populations of Korean pen shell (Atrina pectinata) using microsatellite DNA markers. International Journal of Molecular Sciences, 12: 6024–6039.

    Article  Google Scholar 

  • Bai, Z., Zheng, H., Lin, J., Wang, G., and Li, J., 2013. Comparative analysis of the transcriptome in tissues secreting purple and white nacre in the pearl mussel Hyriopsis cumingii. PLoS One, 8: e53617.

    Article  Google Scholar 

  • Chen, Y., Wu, S., and Pan, S., 2014. Effect of water-soluble chitosan in combination with glutathione on the quality of pen shell adductor muscles. International Journal of Biological Macromolecules, 72: 1250–1253.

    Article  Google Scholar 

  • Chistiakov, D. A., Hellemans, B., and Volckaert, F. A., 2006. Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics. Aquaculture, 255: 1–29.

    Article  Google Scholar 

  • DOF (Department of Fisheries), 2014. China Fisheries Statistic Yearbook. China Agriculture Press, Beijing, 29pp.

    Google Scholar 

  • Fu, H., Wu, Y., Gong, Y., Jiang, S., Xiong, Y., Qiao, H., Cheng, L., Tong, J., and Li, M., 2010. Isolation and characterization of 15 polymorphic microsatellite markers for comb pen shell (Atrina pectinata). Aquaculture Research, 41: e703–e705.

    Article  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., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad- Toh, K., Friedman, N., and Regev, A., 2011. Trinity: Reconstructing a full-length transcriptome without a genome from rna-seq data. Nature Biotechnology, 29: 644–652.

    Article  Google Scholar 

  • Hedgecock, D., Perry, G. M. L., and Voigt, M. L., 2007. Mapping heterosis QTL in the Pacific oyster Crassostrea gigas. Aquaculture, 272: S267–S268.

    Article  Google Scholar 

  • Jiang, Q., Li, Q., Yu, H., and Kong, L., 2014. Genome-wide analysis of simple sequence repeats in marine animals–A comparative approach. Marine Biotechnology, 16: 604–19.

    Article  Google Scholar 

  • Lemer, S., Saulnier, D., Gueguen, Y., and Planes, S., 2015. Identification of genes associated with shell color in the blacklipped pearl oyster, Pinctada margaritifera. BMC Genomics, 16: 1–14.

    Article  Google Scholar 

  • Li, J., Li, J., Chen, P., Liu, P., and He, Y., 2015. Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: Assembly, annotation and marker discovery. Molecular Biology Reports, 42: 135–147.

    Article  Google Scholar 

  • Li, Q., Xu, K., and Yu, R., 2007. Genetic variation in Chinese hatchery populations of the Japanese scallop (Patinopecten yessoensis) inferred from microsatellite data. Aquaculture, 269: 211–219.

    Article  Google Scholar 

  • Liu, H., Zheng, H., Zhang, H., Deng, L., Liu, W., Wang, S., Meng, F., Wang, Y., Guo, Z., Li, S., and Zhang, G., 2015. A de novo transcriptome of the noble scallop, Chlamys nobilis, focusing on mining transcripts for carotenoid-based coloration. BMC Genomics, 16: 44.

    Article  Google Scholar 

  • Liu, J., Li, Q., Kong, L., and Zheng, X., 2011. Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): High divergence and hybridization revealed by molecular and morphological data. Molecular Ecology, 20: 4332–4345.

    Article  Google Scholar 

  • Mandal, S., Jena, J. K., Singh, R. K., Mohindra, V., Lakra, W. S., Deshmukhe, G., Pathak, A., and 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: 1–8.

    Article  Google Scholar 

  • Rosewater, J., 1961. The family Pinnidae in the Indo-Pacific. Indo-Pacific Mollusca, 1: 175–226.

    Google Scholar 

  • Serapion, J., Kucuktas, H., Feng, J., and Liu, Z., 2004. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Marine Biotechnology, 6: 364–377.

    Article  Google Scholar 

  • Shi, M., Lin, Y., Xu, G., Xie, L., Hu, X., Bao, Z., and Zhang, R., 2013. Characterization of the zhikong scallop (Chlamys farreri) mantle transcriptome and identification of biomineralizationrelated genes. Marine Biotechnology, 15: 706–715.

    Article  Google Scholar 

  • Suck, A. H., Lee, J. W., and Dong, C. M., 2012. Population genetic structure of Korean pen shell (Atrina pectinata) in Korea inferred from microsatellite marker analysis. Genes & Genomics, 34: 681–688.

    Article  Google Scholar 

  • Sun, X., Yang, A., Wu, B., Zhou, L., and Liu, Z., 2015. Characterization of the mantle transcriptome of yesso scallop (Patinopecten yessoensis): Identification of genes potentially involved in biomineralization and pigmentation. PLoS One, 10: e0122967.

    Article  Google Scholar 

  • Tóth, G., Gáspári, Z., and Jurka, J., 2000. Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Research, 10: 967–981.

    Article  Google Scholar 

  • Varshney, R. K., Sigmund, R., Börner, A., Korzun, V., Stein, N., Sorrells, M. E., Langridged, P., and Granera, A., 2005. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science, 168: 195–202.

    Article  Google Scholar 

  • Xue, D. X., Wang, H. Y., Zhang, T., and Liu, J. X., 2014. Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers. PLoS One, 9: e95436–e95436.

    Article  Google Scholar 

  • Yamini, K. N., Ramesh, K., Naresh, V., Rajendrakumar, P., Anjani, K., and Kumar, V. D., 2013. Development of ESTSSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.). Journal of Plant Biochemistry and Biotechnology, 22: 90–102.

    Article  Google Scholar 

  • Zeng, X. L., Pang, T. S., and Chen, X. H., 2005. The artificial breeding of Atrina peclinala Linneaus. Marine Sciences, 8: 53–55 (in Chinese).

    Google Scholar 

  • Zhong, X., Li, Q., Guo, X., Yu, H., and Kong, L., 2014. QTL mapping for glycogen content and shell pigmentation in the Pacific oyster Crassostrea gigas using microsatellites and SNPs. Aquaculture International, 22: 1877–1889.

    Article  Google Scholar 

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Acknowledgements

This work was supported by the grants from Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, P. R. China (No. 2016LMFS-B02), the Key Research and Development Program of Shandong Province (No. 2016GSF115012), Basic Scientific Research Fund of YSFRI (No. 2060302201516054), and Natural Science Foundation of Shandong Province (No. ZR2016 CQ32).

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Authors and Affiliations

  1. Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, P. R. China

    Xiujun Sun, Dongming Li, Zhihong Liu, Liqing Zhou, Biao Wu & Aiguo Yang

  2. Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, P. R. China

    Xiujun Sun, Dongming Li, Zhihong Liu, Liqing Zhou, Biao Wu & Aiguo Yang

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  1. Xiujun Sun
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  2. Dongming Li
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  3. Zhihong Liu
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  4. Liqing Zhou
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  5. Biao Wu
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  6. Aiguo Yang
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Correspondence to Aiguo Yang.

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Sun, X., Li, D., Liu, Z. et al. De novo assembly of pen shell (Atrina pectinata) transcriptome and screening of its genic microsatellites. J. Ocean Univ. China 16, 882–888 (2017). https://doi.org/10.1007/s11802-017-3274-z

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  • DOI: https://doi.org/10.1007/s11802-017-3274-z

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