Abstract
Amphioctopus fangsiao is one of the most economically important species and has been considered to be a candidate for aquaculture. In order to facilitate its fine-scale genetic analyses, we constructed a normalized full-length library successfully and developed a set of microsatellite markers in this study. The normalized full-length library had a storage capacity of 6.9×105 independent clones. The recombination efficiency was 95% and the average size of inserted fragments was longer than 1000 bp. A total of 3440 high quality ESTs were obtained, which were assembled into 1803 unigenes. Of these unigenes, 450 (25%) were assigned into 33 Gene Ontology terms, 576 (31.9%) into 153 Kyoto Encyclopedia of Genes and Genomes pathways, and 275 (15.3%) into 22 Clusters of Orthologous Groups. Seventy-six polymorphic microsatellite markers were identified. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosities varied between 0.167 and 0.967 and between 0.326 and 0.944, respectively. Twelve loci were significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no linkage disequilibrium was found between different loci. This study provided not only a useful resource for the isolation of the functional genes, but also a set of informative microsatellites for the assessment of population structure and conservation genetics of A. fangsiao.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J. H., Zhang, Z., Miller, W., and Lipman, D. J., 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25: 3389–3402.
Botsein, D., White, R. L., Skolnick, M., and Davis, R. W., 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32: 314–331.
De Luca, D., Catanese, G., Fiorito, G., and Procaccini, G., 2015. A new set of pure microsatellite loci in the common octopus Octopus vulgaris Cuvier, 1797 for multiplex PCR assay and their cross-amplification in O.maya Voss & Solís Ramírez, 1966. Conservation Genetics Resources, 7: 299–301.
Dieringer, D., and Schlötterer, C., 2003. Microsatellite analyser (MSA): A platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3: 167–169.
Domínguez-Contreras, J. F., Munguía-Vega, A., Ceballos-Vázquez, B. P., Arellano-Martínez, M., and Culver, M., 2014. Characterization of microsatellite loci from two-spotted octopus Octopus bimaculatus Verrill 1883 from pyrosequencing reads. Conservation Genetics Resources, 6: 465–468.
Dong, Z., 1988. Fauna Sinica: Phylum Mollusca. Class Cephalopoda. Science Press, Beijing, 174-176.
Gao, X. L., Zheng, X. D., and Li, Q., 2013. Development and characterization of twelve polymorphic microsatellite loci in the cephalopod Amphioctopus fangsiao (d’Orbigny, 1839–1841). Conservation Genetics Resources, 5: 619–621.
Gotz, S., Garcia-Gomez, J. M., Terol, J., Williams, T. D., Nagaraj, S. H., Nueda, M. J., Robles, M., Talon, M., Dopazo, J., and Conesa, A., 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research, 36: 3420–3435.
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. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29: 644–652.
Li, J. J., and Li, Q., 2008. A set of microsatellite markers for use in the endangered sea urchin Strongylocentrotus nudus developed from S.purpuratus ESTs. Conservation Genetics, 9: 743–745.
Li, Q., and Wan, M. J., 2005. SSRHunter: Development of a local searching software for SSR sites. Hereditas, 27: 808–810.
Lu, C. C., Zheng, X. D., and Lin, X. Z., 2012. Diversity of Cephalopoda from the waters of the Chinese mainland and Taiwan. In: Proceeding of the 1st Mainland and Taiwan Symposium on Marine Biodiversity Studies. Ocean Press, Beijing, 76-87.
Ma, J., Zhang, T., Zhuang, P., Zhang, L. Z., and Liu, T., 2011. Annotation and analysis of expressed sequence tags (ESTs) from Chinese sturgeon (Acipenser sinensis) pituitary cDNA library. Marine Genomics, 4: 173–179.
Marshall, T. C., Slate, J., Kruuk, L. E. B., and Pemberton, M. J., 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7: 639–655.
Mohanty, P., Sahoo, L., Parida, K., and Das, P., 2013. Development of polymorphic EST-SSR markers in Macrobrachium rosenbergii by data mining. Conservation Genetics Resources, 5: 133–136.
Rice, P., Longden, I., and Bleasby, A., 2000. EMBOSS: The European molecular biology open software suite. Trends in Genetics, 16: 276–277.
Rousset, F., 2008. Genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8: 103–106.
Sun, G. H., Liu, X. Q., Ren, L. H., Yang, J. M., Wei, X. M., and Yang, J. L., 2014. Construction of a full-length cDNA library of Solen grandis Dunker and identification of defense-and immune-related genes. Journal of Ocean University of China, 13: 1–5.
Varshney, R. K., Graner, A., and Sorrells, M. E., 2005. Genic microsatellite markers in plants: Features and applications. Trends in Biotechnology, 23: 48–55.
Wang, W. J., Dong, G., Yang, J. M., Zheng, X. D., Wei, X. M., and Sun, G. H., 2015. The development process and seasonal changes of the gonad in Octopus ocellatus Gray off the coast of Qingdao, Northeast China. Fisheries Science, 81: 309–319.
Yu, Z. N., Wang, Y. H., and Fu, D. K., 2010. Development of fifty-one novel EST-SSR loci in the pacific oyster Crassostrea gigas by data mining from the public EST database. Conservation Genetics Resources, 2: 13–18.
Zhang, L. G., Yang, J. M., Liu, X. Q., Wang, W. J., Sun, G. H., Liu, L. J., and Zheng, X. D., 2009. Genetic diversity of Octopus ocellatus by AFLP markers. Oceanologia et Limnologia Sinica, 40: 803–807.
Acknowledgements
This study was supported by the National Natural Science Foundation of China (Nos. 31302215, 31272643), the Shandong Provincial Natural Science Foundation (Nos. BS2014NY010, ZR2013CQ030), and the Shandong Provincial Primary Research and Development Projects (No. 2015GNC110017).
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Feng, Y., Liu, W., Xu, X. et al. Construction of a normalized full-length cDNA library of cephalopod Amphioctopus fangsiao and development of microsatellite markers. J. Ocean Univ. China 16, 897–904 (2017). https://doi.org/10.1007/s11802-017-3291-y
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11802-017-3291-y