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Population genetic structure of Semisulcospira gottschei: simultaneous examination of mtDNA and microsatellite markers

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Abstract

Semisulcospira gottschei is an Asian endemic species inhabiting Korea and China. However, genetic structure analysis of the resource management of this species has not been performed. To investigate the genetic diversity among populations, microsatellites can be used to determine the geographic origins of marine and freshwater species. This study investigated the genetic structures of the Korean and Chinese populations of S. gottschei based on mitochondrial DNA (mtDNA) Cytochrome oxidase subunit I (COI) and polymorphic microsatellite loci developed from Semisulcospira coreana. Analysis of the mtDNA COI sequence revealed 43 haplotypes, which indicated no gene flow between the Korean and Chinese populations. To further elucidate the genetic structures of the Korean and Chinese populations, the population genetics of S. gottschei were analyzed using nine microsatellite markers. The genetic diversity analysis showed an average of 5.25 alleles per locus, with an average allelic richness of 4.02. Excessive homozygosity was found at all loci, which was expected to be due to the presence of null alleles at all loci. Populations of S. gottschei formed two separate clusters according to pairwise FST and AMOVA. Also, the UPGMA tree, PCA, STRUCTURE, and GeneClass indicated separation of the 11 populations into two clusters: Korea and China. These results have potential use in the management, restoration, and distinction of the origin country of populations.

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Data availability

All data generated and/or analyzed during this study are included in this published article. Data available on request from the authors.

References

  1. Chiu YW, Bor H, Kuo PH, Hsu KC, Tan MS, Wang WK, Lin HD (2017) Origins of Semisulcospira libertina (gastropoda: semisulcospiridae) in Taiwan. Mitochondrial DNA A 28:518–525

    CAS  Google Scholar 

  2. Davis GM (1969) A taxonomic study of some species of Semisulcospira in Japan (Mesogastropoda: Pleuroceridae). Malacologia 7:211–294

    Google Scholar 

  3. Sydes MA, Peakall R (1998) Extensive clonality in the endangered shrub Haloragodendron lucasii (Haloragaceae) revealed by allozyme and RAPDs. Mol Ecol 7:87–92

    Google Scholar 

  4. Moon SK, Kim IS, Lim CW, Yoon NY, Jeong BY (2015) Proximate and fatty acid compositions of commercial domestic and imported melania snails Semisulscospira sp. Korean J Fish Aquat Sci 48:977–981

    CAS  Google Scholar 

  5. Rasmussen RS, Morrissey MT (2008) DNA-based methods for the identification of commercial fish and seafood species. Compr Rev Food Sci Food Saf 7:280–295

    CAS  PubMed  Google Scholar 

  6. Planes S, Fauvelot C (2002) Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean. Evolution 56:378–399

    CAS  PubMed  Google Scholar 

  7. Roe KJ, Hartfield PD, Lydeard C (2001) Phylogeographic analysis of the threatened and endangered superconglutinate-producing mussels of the genus Lampsilis (Bivalvia: Unionidae). Mol Ecol 10:2225–2234

    CAS  PubMed  Google Scholar 

  8. Toro JE, Ojeda JA, Vergara AM (2004) The genetic structure of Mytilus chilensis (Hupe 1854) populations along the Chilean coast based on RAPDs analysis. Aquac Res 35:1466–1471

    CAS  Google Scholar 

  9. Kong L, Li Q (2007) Genetic comparison of cultured and wild populations of the clam Coelomactra antiquata (Spengler) in China using AFLP markers. Aquaculture 271:152–161

    CAS  Google Scholar 

  10. Gruenthal KM, Acheson LK, Burton RS (2007) Genetic structure of natural populations of California red abalone (Haliotis rufescens) using multiple genetic markers. Mar Biol 152:1237–1248

    Google Scholar 

  11. Dong YH, Yao HH, Sun CS, Lv DM, Li MQ, Lin ZH (2016) Development of polymorphic SSR markers in the razor clam (Sinonovacula constricta) and cross-species amplification. Genet Mol Res. https://doi.org/10.4238/gmr.15017285

    Article  PubMed  Google Scholar 

  12. Kang JH, Kang HS, Noh ES, Park JY, An CM (2014) Isolation and characterization of novel microsatellite markers for the northern mauxia shrimp, Acetes chinensis, using pyrosequencing. Mar Genomics 18:67–69

    PubMed  Google Scholar 

  13. Hauser L, Adcock GJ, Smith PJ, Ramírez JHB, Carvalho GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc Nat Acad Sci USA 99:11742–11747

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Allendorf FW, England PR, Luikart G, Ritchie PA, Ryman N (2008) Genetic effects of harvest on wild animal populations. Trends Ecol Evol 23:327–337

    PubMed  Google Scholar 

  15. An HS, Lee YG, Park JY, Lee C (2009) Genetic characterization of four East Asian giant scallop (Mizuhopecten yessoensis) populations using microsatellite markers. Aquac Res 40:619–624

    Google Scholar 

  16. Ball AO, Sedberry GR, Zatcoff MS, Chapman RW, Carlin JL (2000) Population structure of the wreckfish Polyprion americanus determined with microsatellite genetic markers. Mar Biol 137:1077–1090

    CAS  Google Scholar 

  17. Gross R, Palm S, Koiv K, Prestegaard T, Jussila J, Paaver T, Geist J, Kokko H, Karjalainen A, Edsman L (2013) Microsatellite markers reveal clear geographic structuring among threatened noble crayfish (Astacus astacus) populations in Northern and Central Europe. Conserv Genet 14:809–821

    CAS  Google Scholar 

  18. Rooker JR, Secor DH, Zdanowicz VS, DeMetrio G, Relini LO (2003) Identification of northern bluefin tuna stocks from putative nurseries in the Mediterranean Sea and western Atlantic Ocean using otolith chemistry. Fish Oceanogr 12:75–84

    Google Scholar 

  19. Yamashita Y, Omura Y, Okazaki E (2006) Distinct regional profiles of trace element content in muscle of Japanese eel Anguilla japonica from Japan, Taiwan, and China. Fish Sci 72:1109–1113

    CAS  Google Scholar 

  20. Kang JH, Noh ES, Park JY, An CM, Choi JH, Kim JK (2015) Rapid origin determination of the northern mauxia shrimp (Acetes chinensis) based on allele specific polymerase chain reaction of partial mitochondrial 16S rRNA gene. Asian–Australas J Anim Sci 28:568–572

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Park YJ, Noh ES, Park JY, Kim EM, Noh JK, Choi TJ, Kang JH (2018) Development of a simple, rapid multiplex PCR method using the 16S rRNA gene to determine the country of origin of brackish water bivalve Corbicula japonica. Food Anal Methods 11:3034–3041

    Google Scholar 

  22. Takashima Y, Morita T, Yamashita M (2006) Complete mitochondrial DNA sequence of Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T. trachurus and T. japonicus using PCR-RFLP. Fish Sci 72:1054–1065

    CAS  Google Scholar 

  23. Rahman MT, Uddin MS, Sultana R, Moue A, Setu M (2013) Polymerase chain reaction (PCR): a short review. AKMMC J 4:30–36

    CAS  Google Scholar 

  24. Park YJ, Lee MN, Kim EM, Park JY, Noh JK, Choi TJ, Kang JH (2019) Development and characterization of novel polymorphic microsatellite markers for the Korean freshwater snail Semisulcospira coreana and cross-species amplification using next-generation sequencing. J Oceanol Limnol 38:1–6

    CAS  Google Scholar 

  25. Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  26. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3.2). Accessed 27 Sep 2012

  27. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

    PubMed  Google Scholar 

  28. Langella O (2007) Populations 1.2.3.0: population genetic software (individuals or population distances, phylogenetic trees). http://bioinformatics.org/~tryphon/populations/

  29. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS  PubMed  Google Scholar 

  31. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GENECLASS2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539

    CAS  PubMed  Google Scholar 

  32. Miura O, Köhler F, Lee T, Li J, Ó Foighil D (2013) Rare, divergent Korean Semisulcospira spp. mitochondrial haplotypes have Japanese sister lineages. J Molluscan Stud 79:86–89

    Google Scholar 

  33. Xu Z, Primavera JH, De La Pena LD, Pettit P, Belak J, Alcivar-Warren A (2001) Genetic diversity of wild and cultured black tiger shrimp (Penaeus monodon) in the Philippines using microsatellites. Aquaculture 199:13–40

    CAS  Google Scholar 

  34. Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629

    PubMed  Google Scholar 

  35. Gu Q, Xiong B, Zhu Y, Wang Q, Shi P (2012) Isolation and characterization of polymorphic microsatellites loci in the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda). Conserv Genet Resour 4:387–390

    Google Scholar 

  36. Vadopalas B, Leclair LL, Bentzen P (2004) Microsatellite and allozyme analyses reveal few genetic differences among spatially distinct aggregations of geoduck clams (Panopea abrupta, Conrad 1849). J Shellfish Res 23:693–706

    Google Scholar 

  37. Launey S, Ledu C, Boudry P, Bonhomme F, Naciri-Graven Y (2002) Geographic structure in the European flat oyster (Ostrea edulis L.) as revealed by microsatellite polymorphism. J Hered 93:331–351

    CAS  PubMed  Google Scholar 

  38. Eackles MS, King TL (2002) Isolation and characterization of microsatellite loci in Lampsilis abrupta (Bivalvia: Unionidae) and cross-species amplification within the genus. Mol Ecol Notes 2:559–562

    CAS  Google Scholar 

  39. Barbara T, Palma-Silva C, Paggi GM, Bered F, Fay MF, Lexer C (2007) Cross‐species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol 16:3759–3767

    PubMed  Google Scholar 

  40. Nguema RM, Langand J, Galinier R et al (2013) Genetic diversity fixation and differentiation of the freshwater snail Biomphalaria pfeifferi (Gastropoda Planorbidae) in arid lands. Genetica 141:171–184

    Google Scholar 

  41. Slatkin M (1985) Rare alleles as indicators of gene flow. Evolution 39:53–65

    PubMed  Google Scholar 

  42. Zhan A, Hu J, Hu X, Zhou Z, Hui M, Wang S, Peng W, Wang M, Bao Z (2009) Fine-scale population genetic structure of Zhikong scallop (Chlamys farreri): do local marine currents drive geographical differentiation? Mar Biotechnol 11:223–235

    CAS  Google Scholar 

  43. Lockwood JG (1979) The Antarctic Ice-Sheet: regulator of global climates? Geogr J 145:469–471

    Google Scholar 

  44. Park YC, Kitade O, Schwarz M, Kim JP, Kim W (2006) Intraspecific molecular phylogeny, genetic variation and phylogeography of Reticulitermes speratus (Isoptera: Rhinotermitidae). Mol Cells 21:59–103

    Google Scholar 

Download references

Acknowledgements

This work was supported by Grant from the National Institute of Fisheries Science (R2021038).

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Authors and Affiliations

  1. Biotechnology Research Division, National Institute of Fisheries Science, Pusan, 46083, Republic of Korea

    Yeon-Jung Park, Mi Nan Lee, Jung-Ha Kang, Jung Youn Park, Jae Koo Noh & Eun-Mi Kim

  2. Department of Microbiology, Pukyoung National University, 45, Yongso-ro, Nam-Gu, Pusan, 48513, Republic of Korea

    Tae-Jin Choi

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  1. Yeon-Jung Park
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Park, YJ., Lee, M.N., Kang, JH. et al. Population genetic structure of Semisulcospira gottschei: simultaneous examination of mtDNA and microsatellite markers. Mol Biol Rep 48, 97–104 (2021). https://doi.org/10.1007/s11033-020-05821-9

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  • DOI: https://doi.org/10.1007/s11033-020-05821-9

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