Abstract
Isolation of high molecular weight DNA from gastropod molluscs and its subsequent PCR amplification is considered difficult due to excessive mucopolysaccharides secretion which co-precipitate with DNA and obstruct successful amplification. In an attempt to address this issue, we describe a modified CTAB DNA extraction method that proved to work significantly better with a number of freshwater and terrestrial gastropod taxa. We compared the performance of this method with Qiagen® DNeasy Blood and Tissue Kit. Reproducibility of amplification was verified using a set of taxon-specific primers, wherein modified CTAB extracted DNA could be replicated at least four out of five times but kit extracted DNA could not be replicated. In addition, sequence quality was significantly better with CTAB extracted DNA. This could be attributed to the removal of polyphenolic compounds by polyvinyl pyrrolidone which is the only difference between conventional and modified CTAB DNA extraction methods for animals. The genomic DNA isolated using modified CTAB protocol was of high quality (A260/280 ≥ 1.80) and could be used for downstream reactions even after long-term storage (more than 2 years).
Similar content being viewed by others
References
Aljanabi SM, Martinez I (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res 25:4692–4693. https://doi.org/10.1093/nar/25.22.4692
Aranishi F, Okimoto T (2006) A simple and reliable method for DNA extraction from bivalve mantle. J Appl Genet 47:251–254. https://doi.org/10.1007/BF03194632
Brönmark C (1989) Interactions between epiphytes, macrophytes and freshwater snails: a review. J Molluscan Stud 55:299–311. https://doi.org/10.1093/mollus/55.2.299
Butler AJ (1976) A Shortage of Food for the Terrestrial Snail Helicella virgata in South Australia. Oecologia 25:349–371
Carter MA, Jeffery RCV, Williamson P (1979) Food overlap in co-existing populations of the land snails Cepaea nemoralis (L.) and Cepaea hortensis (Müll). Biol J Linn Soc 11:169–176. https://doi.org/10.1111/j.1095-8312.1979.tb00033.x
Chase JM, Knight TM (2006) Effects of eutrophication and snails on Eurasian watermilfoil (Myriophyllum spicatum) invasion. Biol Invasions 8:1643–1649. https://doi.org/10.1007/s10530-005-3933-7
Cheung WY, Hubert N, Landry BS (1993) A simple and rapid DNA microextraction method for plant, animal, and insect suitable for RAPD and other PCR analyses. Genome Res 3:69–70. https://doi.org/10.1101/gr.3.1.69
Dowell K (2008) Molecular phylogenetics: an introduction to computational methods and tools for analyzing evolutionary relationships. Mol Phylogenetics, pp 1–19. http://www.math.umaine.edu/~khalil/courses/MAT500/papers/MAT500_Paper_Phylogenetics.pdf. Accessed 22 Jan 2020
Fang G, Hammar S, Grumet R (1992) A quick and inexpensive method for removing polyssaccharides from plant genomic DNA. Biotechniques 13:52–56. https://doi.org/10.1080/10643389.2012.728825
Fink P, Von Elert E (2006) Physiological responses to stoichiometric constraints: nutrient limitation and compensatory feeding in a freshwater snail. Oikos 115:484–494
Geiselman JA, McConnell OJ (1981) Polyphenols in brown algae Fucus vesiculosus and Ascophyllum nodosum: chemical defenses against the marine herbivorous snail, Littorina littorea. J Chem Ecol 7:1115–1133. https://doi.org/10.1007/BF00987632
Giribet G (2003) Molecules, development and fossils in the study of metazoan evolution; Articulata versus Ecdysozoa revisited. Zoology 106:303–326. https://doi.org/10.1078/0944-2006-00131
Huelsken T, Schreiber S, Hollmann M (2011) COI amplification success from mucus-rich marine gastropods (Gastropoda: naticidae) depends on DNA extraction method and preserving agent. Mitteilungen der Dtsch Malakozool Gesellschaft 85:17–26
Jaksch K, Eschner A, Rintelen TV, Haring E (2016) DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods. BMC Res Notes 9:1–12. https://doi.org/10.1186/s13104-016-2147-7
John ME (1992) An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Res 20:2381. https://doi.org/10.1093/nar/20.9.2381
Lio P, Goldman N (1998) Models of molecular evolution and phylogeny. Genome Res 8:1233–1244. https://doi.org/10.1101/gr.8.12.1233
March JG, Pringle CM, Townsend MJ, Wilson AI (2002) Effects of freswater shrimp assemblages on benthic communities along an altitudinal gradient of a tropical stream. Freshw Biol 47:377–390
Martin SM (2000) Terrestrial snails and slugs (Mollusca: Gastropoda) of maine. Northeast Nat 7:33–88
Mason CF (1970) Food, feeding rates and assimilation in woodland snails. Oecologia 4:358–373
Palumbi S, Martin A, Romano S et al (2002) The simple fool’s guide to PCR. Department of Zoology and Kewalo Marine Laboratory, University of Hawaii
Pereira JC, Chaves R, Bastos E et al (2011) An efficient method for genomic DNA extraction from different molluscs species. Int J Mol Sci 12:8086–8095. https://doi.org/10.3390/ijms12118086
Poonam Tripathi NK, Kaur P, Kumari A (2013) Optimization of DNA isolation and PCR protocol for rapd analysis from mucopolysaccharide rich foot muscles of Lymnaea acuminata (Gastropoda: Pulmonata) from Indian Himalayan regions. Int J Zool Res 3:35–42
Popa OP, Murariu D, Popa LO (2007) Comparison of four DNA extraction methods from invasive freshwater bivalve species (Mollusca, Bivalvia) in Romanian Fauna. Trav du Muséum Natl d’Histoire Nat «Grigore Antipa» 50:527–536
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15. https://doi.org/10.1007/BF02772108
Rowland LJ (1993) Use of polyethylene glycol for purification of DNA from leaf tissue of woody plants. BioTechniques 14:735–736
Sidow A, Bowman BH (1991) Molecular phylogeny. Curr Opin Genet Dev 1:451–456. https://doi.org/10.1016/S0959-437X(05)80191-1
Skujiene G, Soroka M (2003) A comparison of different DNA extraction methods for slugs (Mollusca: Pulmonata). Ekologija 1:12–16
Sokolov EP (2000) An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues. J Molluscan Stud 66:573–575. https://doi.org/10.1093/mollus/66.4.573
Speiser B, Rowell-Rahier M (1991) Effects of food availability, nutritional value, and alkaloids on food choice in the generalist herbivore Arianta arbustorum (Gastropoda: Helicidae). Oikos 62:306–318
Steinberg PD (1988) Effects of quantitative and qualitative variation in phenolic compounds on feeding in three species of marine invertebrate herbivores. J Exp Mar Bio Ecol 120:221–237. https://doi.org/10.1016/0022-0981(88)90003-2
Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 51:689–702. https://doi.org/10.1080/10635150290102456
Vaughn CC, Gelwick FP, Matthews WJ (1993) Effects of algivorous minnows on production of grazing stream invertebrates. Oikos 66:119–128
Wade CM, Mordan PB, Naggs F (2006) Evolutionary relationships among pulmonate land snails and slugs (Pulmonata. Stylommatophora). Biol J Linn Soc 87:593–610. https://doi.org/10.1111/j.1095-8312.2006.00596.x
Williams ST, Reid DG, Littlewood DTJ (2003) A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): Unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean. Mol Phylogenet Evol 28:60–86. https://doi.org/10.1016/S1055-7903(03)00038-1
Winnepenninckx B, Backeljau T, De Wachter R (1993) Extraction of high molecular weight DNA from molluscs. Trends Genet 9:407. https://doi.org/10.1016/0168-9525(93)90102-N
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Nat Acad Sci. https://doi.org/10.1073/pnas.0913022107
Yue GH, Orban L (2005) A simple and affordable method for high-throughput DNA extraction from animal tissues for polymerase chain reaction. Electrophoresis 26:3081–3083. https://doi.org/10.1002/elps.200410411
Acknowledgements
Authors would like to thank Department of Science and Technology, Government of India (Grant No. EMR_2015/000199/v1/21385) for funding. We would also like to thank Dr. Suzanne Williams, Dr. Praveen Karanth, Dr. Maitreya Sil for help in developing the protocol.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Chakraborty, S., Saha, A. & Neelavar Ananthram, A. Comparison of DNA extraction methods for non-marine molluscs: is modified CTAB DNA extraction method more efficient than DNA extraction kits?. 3 Biotech 10, 69 (2020). https://doi.org/10.1007/s13205-020-2051-7
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-020-2051-7