تنوع ژنتیکی و ساختار جمعیتی سخت پوست Paramysis intermedia در مناطق تیاب و خلیج گواتر با استفاده از توالی یابی ژن میتوکندریایی 16SrRNA

نوع مقاله: مقاله پژوهشی

نویسندگان

1 دانشجوی کارشناسی ارشد-گروه شیلات، دانشکدة علوم و فنون دریایی و جوی، دانشگاه هرمزگان

2 استادیار گروه شیلات، دانشکدة علوم و فنون دریایی و جوی، دانشگاه هرمزگان

3 استادیار بخش ژنتیک، پژوهشکدة اکولوژی خلیج فارس و دریای عمان، هرمزگان

4 کارشناس ارشد بخش ژنتیک و اصلاح نژاد، پژوهشکدة آبزی‌پروری آب‌های داخلی، بندر انزلی

چکیده

یکی از مهم‌ترین زئوپلانکتون‌هایی که در نواحی مصبی و دریایی مورد تغذیة آبزیان قرار می‌گیرد سخت‌پوست پارامایسیس اینترمدیا Paramysis intermedia است. با توجه به وجود ذخایر این زئوپلانکتون در خلیج فارس و دریای عمان، آگاهی از ساختار ژنتیکی آن به منظور حفظ تنوع زیستی و خزانة ژنی دارای اهمیت است. در پژوهش حاضر برای اولین‌بار ساختار ژنتیکی و جمعیتی سخت‌پوست پارامایسیس اینترمدیا در دو منطقة تیاب و خلیج گواتر با استفاده از توالی‌یابی ژن 16S rRNA میتوکندریایی بررسی شد. نتایج ده نمونة توالی‌یابی‌شده شامل 365 باز هم‌ردیف‌شدة ژن 16S rRNA، 339 جایگاه ژنی مونومورف، 26 جایگاه ژنی پلی‌مورف و 27 موتاسیون نشان‌دهندة نرخ بسیار کم موتاسیون در این گونه بین مناطق مورد مطالعه بود. هیچ گونه چندشکلی اضافه و حذف مشاهده نشد. تعداد نه‌ هاپلوتیپ در دو منطقه به دست آمد و میزان تنوع هاپلوتیپی و تنوع نوکلئوتیدی برای تمامی نمونه‌ها بین دو منطقه به ترتیب 003/0 ± 978/0 و 000/0 ± 035/0 محاسبه شد. مقدار هتروزایگوسیتی مورد انتظار برای منطقة تیاب بیشتر (184/0 ± 287/0) از خلیج گواتر (088/0 ± 014/0) بود. مقدار Fst در سطح احتمال 05/0 بین دو جمعیت 18/0 و معنی‌دار بود و در ترسیم درخت فیلوژنتیکی این جدایی به‌وضوح دیده شد. میانگین مقدار آزمون Tajima's D و Fu's FS بین دو منطقه به ترتیب 12/0- و 51/2 و غیر معنی‌دار بود که نشان‌دهندة نبود بسط جمعیتی بین نمونه‌های دو منطقه است. نتایج نشان داد که سخت‌پوست پارامایسیس اینترمدیا در دو منطقة مطالعه‌شده، به خصوص منطقة تیاب، از تنوع ژنتیکی بالایی برخوردار است و هر یک جمعیت مستقلی دارند.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Genetic diversity and population structure of crustacean Paramysis intermedia in Tiab and Gwatr Bay regions using mitochondrial 16S rRNA gene sequencing

نویسندگان [English]

  • Samira Vahidinejad 1
  • Iman Sourinejad 2
  • Saeid Tamadoni Jahromi 3
  • Arash Akbarzadeh 2
  • Fariba Keshavarzi 1
  • Fereidon Chakmehdouz Ghasemi 4
1 MSc. Fisheries Department, Faculty of Marine and Atmospheric Science and Technology, University of Hormozgan, Iran
2 Assistant Professor, Fisheries Department, Faculty of Marine and Atmospheric Science and Technology, University of Hormozgan, Iran
3 Assistant Professor, Genetics Department, Persian Gulf and Oman Sea Research Center, Hormozgan Province, Iran
4 MSc. Genetics Department, Inland Aquaculture Research Institute, Anzali Port, Iran
چکیده [English]

The crustacean Paramysis intermedia is one of the most important zooplanktons which is used as food by aquatic animals in estuaries and marine environments. Regarding the existence of this zooplankton stocks in the Persian Gulf and Oman Sea, knowledge on genetic structure of this species is necessary for conservation of its biological diversity and gene pool. In present study, genetic diversity and population structure of Paramysis intermedia collected from Tiab and Gwatr Bay regions was assessed for the first time by mitochondrial 16S rRNA sequencing. Analysis of 10 sequenced samples including 365 alligned base pairs of 16S rRNA yielded 339 monomorphic loci, 26 polymorphic loci and 27 mutations, indicating a very low ratio of mutation between the two studied regions in this species. No insertions and deletions were observed. Nine haplotypes were identified in these two regions and haplotype and nucleotide diversity were 0.978±0.003 and 0.035±0.000, respectively for all samples between regions. Expected heterozygosity for Tiab region was higher (0.287±0.164) than Gwatr Bay (0.014±0.088). Based on the F- statistic parameter, population genetic distance was 0.18 between samples of the regions and was significant (P<0.05). According to the analysis of phylogenetic tree, the separation between the samples of the two regions was obvious. Mean values of Tajima’s D and Fu’s Fs between the two regions were -0.12 and 2.51, respectively. No significant values of these tests are indicative of no population expansion between the two regions of Tiab and Gwatr Bay. According to the results of this study, Paramysis intermedia populations of these regions have high genetic diversity especially in Tiab and each of its two populations is a genetically differentiated comunity.

کلیدواژه‌ها [English]

  • Gwatr bay
  • Paramysis intermedia
  • sequencing
  • Tiab
  • 16S rRNA
[1]. Anahid, T., Sajjadi, M.M., Kamrani, E., Nazari Bajgan, A., 2012. Nutritional value investigation of Mysids from shrimp culture ponds of Hormozgan province and the effect of some environmental factors on their survival. M.Sc. thesis of Fisheries, Hormozgan University, 63p (In Persian).

[2]. Avise, J.C., 2000. Phylogeography the history and formation of species. Harward University Press, Cambridge, 447p.

[3]. Beacham, T.D., Mcintosh, M., MacConnachie, C., 2004. Population structure of lake-type and river-type sockeye salmon in Transboundary rivers of northern British Columbia. Journal of Fish Biology 65, 389-402.

[4]. Bilton, D.T., Paula, J., Bishop, J.D.D., 2002. Dispersal, genetic differentiation and speciation in estuarine organisms. Estuarine, Coastal and Shelf Science 55, 937-952.

[5]. Bruford, M., Bradley, D., Luikart, G., 2003. DNA markers reveal the complexity of livestock domestication. Nature Reviews Genetics 3, 900-910.

[6]. Bucklin, A., Wiebe, P.H., 1998. Low mitochondrial diversity and small effective population sizes on the copepods Calanus finmarchicus and Nannocalanus minor: possible impact of climate variation during recent glaciation. Journal of heredity 89, 383-392.

[7]. Calo-Mata, P., Pascoal, A., Fernandez, I., Bohme, K., Gallardo, J., 2009. Evaluation of a novel 16S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea. Analytical Biochemistry 391(2), 127-134.

[8]. Cognetti, G., Maltagliati, F., 2004. Strategies of genetic biodiversity conservation in the marine environment. Marine Pollution Bulletin 48, 811-812.

[9]. Defew, L.H., Mair, J.M., Guzman, H.M., 2005. An assessment of metal contamination in mangrove sediments and leaves from Punta Mala Bay, Pacific Panama. Marine Pollution Bulletin 50, 547-552.

[10]. Deprez, T., Vanden Berghe, E., Vincx, M., 2004. NeMys: a multidisciplinary biological information system. In: VandenBerghe, E., Brown, M., Costello, M., Heip, C., Levitus, S., Pissierssens, P. (Eds). Proceedings of “The colour of ocean data”: international symposium on oceanographic data and information management with special attention to biological data. Brussels, Belgium. IOC Workshop Report (UNESCO, Paris), 188, 57-63.

[11]. Diz, P.A., Presa, P., 2009. The genetic diversity pattern of Mytilus alloprovincialis in Galicia Rías (NW Iberian estuaries). Aquaculture 287, 278-285.

[12]. Excoffier, L., Smouse, P.E., Quattro, J.M., 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479-49.

[13]. Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925.

[14]. Hamzeh, M.A., Boumeri, M., Rezaei, H., Baskaleh, G.R., 2011. Environmental geochemistry of heavy metals in coastal sediments of Gwatr bay, southeastern Iran. Oceanography 2(8), 11-20 (In Persian).

[15]. Harbison, P., 1986. Mangrove muds: a sink or source for trace metals. Marine Pollution Bulletin 17, 246-250.

[16]. Harris, R.R., Santos, M.C.F., 2000. Heavy metal contamination and physiological variability in the Brazilian mangrove crabs, Ucides cordatus and Callinectes danoe (Crustacea: Decapoda). Marine Biology 137, 691-703.

[17]. Kimura, M., 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111-120.

[18]. Liu, Z.J., Cordes, J.F., 2004. DNA marker technological and their applications in aquaculture genetics. Aquaculture 38, 1-37.

[19]. Nei, M., 1978. Estimation of average heterozygosity and Genetic distance from a small number of individuals. Genetics 89, 583-590.

[20]. Ogonowski, M., Hansson, S., Duberg, J., 2013. Status and vertical size distributions of a pelagic mysid community in the northern Baltic proper. Boreal Environment research 18, 1-8.

[21]. Palumbi, S., Martin, R.A., Romano, S., McMillan, W.O., Stice, L., Grabowski, G., 1991. The simple fool’s Guide to PCR, Version 2. University of Hawaii Zoology Department, Honululu, 94p.

[22]. Peijnenburg, K.T.C., Breeuwer, J.A.J., Pierrot-Bults, A.C., Menken, S.B.J., 2004. Phylogeography of the planktonic chaetogenath Sagitta setosa reveals isolation in European seas. Evolution 58, 1472-1487.

[23]. Pinera, J.A., Blanco, G., Vázquez, E., Sánchez, J.A., 2007. Genetic diversity of black spot seabream (Pagellus bogaraveo) populations Spanish Coasts: a preliminary study. Marine Biology 151, 2153-2158.

[24]. Remerie, T., Bourgois, T., Peelaers, D., Vierstraete, A., Vanfleteren, J.R., Vanreusel, A., 2006. Phylogeographic patterns of the mysid Mesopodopsis slabberi (Crustacea, Mysida) in Western Europe: evidence for high molecular diversity and cryptic speciation. Marine Biology 149, 465-481.

[25]. Remerie, T., Bourgois, T., Vanreusel, A., 2005. Morphological differentiation between geographically separated populations of Neomysis integer and Mesopodopsis slabberi (Crustacea, Mysida). Hydrobiologia 549, 239-250.

[26]. Remerie, T., Vierstraete, A., Weekers, P.H.H., Vanfleteren, J.R., Vanreusel, A., 2009. Phylogeography of an estuarine mysid, Neomysis integer (Crustacea, Mysida), along the north-east Atlantic coasts. Journal of Biogeography 36, 39-54.

[27]. Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X., Rozas, R., 2003. DnaSP, DNA polymorphism analyses by thecoalescent and other methods. Bioinformatics 19, 2496-2497.

[28]. Rudstam, L.G., Danielsson, K., Hansson, S., Johansson, S., 1989. Diel vertical migration and feeding Patterns of Mysis mixta (crustacean, mysidacea) in the Baltic Sea. Marine Biology 101, 43-520.

[29]. Slatkin, M., Hudson, R., 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555-562.

[30]. Sole, M., Porte, C., Barcelo, D., Albaiges, J., 2000. Bivalves residue analysis for the assessment of coastal pollution in the Ebro Delta (NW Mediterranean). Marine Pollution Bulletin 40, 746-753.

[31]. Stamatis, C., Triantafyllidis, A., Moutou, K.A., Mamuris. Z., 2004. Mitochondrial DNA variation in Northeast Atlantic and Mediterranean populations of Norway lobster, Nephrops norvegicus. Molecular Ecology 13, 1377-1390.

[32]. Taggart, J.B., Hynes, R.A., Prodohal, P.A., Ferguson, A., 1992. A simplified protocol for routin total DNA isolation from salmonid fishes. Journal of fish biology 40, 963-965.

[33]. Tajima, F., 1989. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.

[34]. Thai, B.T., Pham, T.A., Austin, G.M., 2006. Genetic diversity of common carp in Vietnam using direct sequencing and SSCP analysis of the mitochondrial DNA control region. Aquaculture 258, 228-240.

[35]. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL-X Windows interface: flexible strategies for multiple sequence alignment aided byquality analysis tools. Nucleic Acid Research 2, 4876-4882.

[36]. Valles-Jimenex, R., Gaffney, P.M., Perez-Eniquez, R., 2006. RFLP analysis of the mtDNA control region in white shrimp (Litopenaeus vannamei) population from the eastern pacific. Marine Biology 148, 867-873.

[37]. Virgilio, M., Abbiati, M., 2004. Habitat discontinuity and genetic structure in populations of the estuarine species Hediste diversicolor (Polychaeta: Nereididae). Estuarine, Coastal and Shelf Science 61, 361-367.

[38]. Wang, H., Kesinger, J.W., Zhou, Q., Matrin, G., Turner, S., 2008. Identification and characterization of zebra fish ocular formation genes. Genome 51(3), 222-235.

[39]. Watterson, G.A., 1984. Lines of descent and the coalescent. Theoretical Population Biology 26, 77-93.

[40]. Weersing, K., Toonen, R.J., 2009. Population genetics, larval dispersal, and connectivity in marine systems. Marine Ecology Progress Series 393, 1-12.

[41]. Woods, M.C., Valentino, F., 2003. Frozen mysids as an alternative to live Artemia in culturingseahorses Hippocampus abdominalis. Aquaculture Research 34, 757-763.

[42]. Wright, S., 1978. Evolution and the genetics of populations variability within and among natural populations. University of Chicago Press. 2nd Ed., University of Chicago Press, Chicago, 465p.

[43]. Zardoya, R., Castilho, R., Grande, C., Favre-Krey, L., Caetano, S., Marcato, S., Krey, G., Patarnello, T., 2004. Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean Sea. Molecular Ecology 13, 1785-1798.