Penaeus vannamei broodstock genetic diversity based on 16S rRNA gene mtDNA
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M.Kh. Pazir * , A. Dashtiannasab , S. Kakoolaki , E. Mohammadi , S. Pourmozaffar , I. Hakiminia , A. Hemati  |
Iran Shrimp Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education & Extension Organization (AREEO), Bushehr, Iran. |
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Abstract: (998 Views) |
Based on the 16S rRNA genome of mitochondrial DNA, this study examined the genetic diversity of Penaeus vannamei broodstocks to determine genetic indicators. This study included two populations, High Health (H) and Molokai (M), of the F3 and F5 generations, respectively. Extraction of DNA from samples was performed using a commercial kit. A pair of special primers amplified the 16S rRNA gene. Then, a 16S rRNA fragment of mitochondrial DNA was sequenced. The World Gene Bank has accession numbers LC468129.1 and LC468130.1 for these sequences. Based on the 486 loci identified, there are 484 conserved loci and two variable loci, each of which contains phylogenetic information under parsimony conditions, and 18 singletons. The similarity between LC468129.1 and LC468130.1 with LC121701.1 was 99.49 and 98.99%, respectively. In conclusion, Neighbor-joining algorithms identified each population with accession number LC468129.1 and LC468130.1 with 64% and 66% in separate branches, respectively. |
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Keywords: Penaeus vannamei, 16S rRNA, Genetic indicators, Phylogenetic |
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Full-Text [PDF 463 kb]
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Type of Study: Research |
Subject:
General Received: 2023/01/1 | Accepted: 2022/03/30 | Published: 2022/03/30
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1. Beacham, T.D., Hay, D.E. and Le, K. D., 2005. Population structure and stock identification of eulachon (Thaleichthys pacificus), an anadromous smelt, in the Pacific Northwest. Marine Biotechnology, 7(4), 363-372. Doi: 10.1007/s10126-004-4075-0 [ DOI:10.1007/s10126-004-4075-0] [ PMID] 2. Benzie, J.A.H., Ballment, E., Forbes, A.T., Demetriades, N.T., Sugama, K. and Moria, S., 2002. Mitochondrial DNA variation in Indo‐Pacific populations of the giant tiger prawn, Penaeus monodon. Molecular Ecology, 11(12), 2553-2569. Doi: 10.1046/j.1365-294X.2002.01638.x [ DOI:10.1046/j.1365-294X.2002.01638.x] [ PMID] 3. Bert, T.M. and McMillen-Jackson, A. L., 2004. Genetic Diversity in the mtDNA Control Region and Population Structure in the Pink Shrimp Farfantepenaeus Duorarum. Journal of Crustacean Biology, 24(1), 101-109. Doi: 10.1651/C-2372 [ DOI:10.1651/C-2372] 4. Calo-Mata, P., Pascoal, A., Fernández-No, I., Böhme, K., Gallardo, J.M. and Barros-Velázquez, 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. Doi: 10.1016/j.ab.2009.05.020 [ DOI:10.1016/j.ab.2009.05.020] [ PMID] 5. Chawla, H.S., 2011. Introduction to Plant Biotechnology. CRC Press. Doi: 10.1201/9781315275369 [ DOI:10.1201/9781315275369] 6. de Croos, M.D.S. and Pálsson, S., 2010. Mitochondrial DNA variation and population genetic structure of white shrimp Fenneropenaeus indicus along the coastal belt of Sri Lanka. Aquatic Living Resources, 23(3), 315-323. Doi: 10.1051/alr/2010027 [ DOI:10.1051/alr/2010027] 7. Francisco, A.K. and de, Galetti Junior, P.M., 2005. Genetic distance between broodstocks of the marine shrimp Litopenaeus vannamei (Decapoda, Penaeidae) by mtDNA analyses. Genetics and Molecular Biology, 28(2), 258-261. Doi: 10.1590/S1415-47572005000200014 [ DOI:10.1590/S1415-47572005000200014] 8. Gusmão, J., Lazoski, C. and Solé-Cava, A.M., 2000. A new species of Penaeus (Crustacea: Penaeidae) revealed by allozyme and cytochrome oxidase I analyses. Marine Biology, 137(3), 435-446. Doi: 10.1007/s002270000365 [ DOI:10.1007/s002270000365] 9. Hosseini, S.J., Elahi, E. and Raie, R.M., 2004. The chromosome number of the Persian Gulf shrimp Penaeus semisulcatus. Iranian International Journal of Science, 5, 13-23. 10. Maggioni, R., Rogers, A.D., Maclean, N. and D'Incao, F., 2001. Molecular Phylogeny of Western Atlantic Farfantepenaeus and Litopenaeus Shrimp Based on Mitochondrial 16S Partial Sequences. Molecular Phylogenetics and Evolution, 18(1), 66-73. Doi: 10.1006/mpev.2000.0866 [ DOI:10.1006/mpev.2000.0866] [ PMID] 11. Mendoza-Cano, F., Grijalva-Chon, J. M., Pérez-Enríquez, R., Ramos-Paredes, J. and Varela-Romero, A., 2013. Genetic diversity of mitochondrial DNA from Litopenaeus vannamei broodstock used in northwestern Mexico. Ciencias Marinas, 39(4), 401-412. Retrieved from https://www.scielo.org.mx/scielo.php?script=sci_arttext&pid=S0185-38802013000400006 [ DOI:10.7773/cm.v39i4.2269] 12. Nei, M., 1978. Estımatıon of average heterozygosıty and genetıc dıstance from a small number of ındıvıduals. Genetics, 89(3), 583-590. Doi: 10.1093/genetics/89.3.583 [ DOI:10.1093/genetics/89.3.583] [ PMID] [ PMCID] 13. Noroozi, Z. and Hosseini, S.J., 2015. Evaluation of 5.8 S rRNA to identify Penaeus semisulcatus and its subspecies, Penaeus semisulcatus persicus (Penaeidae) and some Decapoda species. International Journal of Aquatic Biology, 3(4), 274-281. Doi: 10.22034/ijab.v3i4.106 14. Panutrakul, S. and Senanan, W., 2021. Abundance of introduced Pacific whiteleg shrimp Penaeus vannamei (Boone, 1931) along the east coast of Thailand. Aquatic Invasions, 16(4), 750-770. Doi: 10.3391/ai.2021.16.4.10 [ DOI:10.3391/ai.2021.16.4.10] 15. Pazir, M.K., Ahmadi, A. and Khezri, P.H.. 2022. The effect of COVID-19 pandemic on the shrimp industry of Iran. Marine Policy, 136(November 2021), 104900. Doi: 10.1016/j.marpol.2021.104900 [ DOI:10.1016/j.marpol.2021.104900] [ PMID] [ PMCID] 16. Peregrino-Uriarte, A.B., Varela-Romero, A., Muhlia-Almazán, A., Anduro-Corona, I., Vega-Heredia, S., Gutiérrez-Millán, L.E. and Yepiz-Plascencia, G., 2009. The complete mitochondrial genomes of the yellowleg shrimp Farfantepenaeus californiensis and the blue shrimp Litopenaeus stylirostris (Crustacea: Decapoda). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 4(1), 45-53. Doi: 10.1016/j.cbd.2008.10.003 [ DOI:10.1016/j.cbd.2008.10.003] [ PMID] 17. Piñera, J.A., Blanco, G., Vázquez, E. and Sánchez, J.A., 2007. Genetic diversity of blackspot seabream (Pagellus bogaraveo) populations off Spanish Coasts: a preliminary study. Marine Biology, 151(6), 2153-2158. Doi: 10.1007/s00227-007-0665-5 [ DOI:10.1007/s00227-007-0665-5] 18. Ren, S., Prentis, P., Mather, P.B., Li, Y., Tang, B. and Hurwood, D.A., 2020. Genetic parameters for growth and survival traits in a base population of Pacific white shrimp (Litopenaeus vannamei) developed from domesticated strains in China. Aquaculture, 523, 735148. Doi: 10.1016/J.AQUACULTURE.2020.735148 [ DOI:10.1016/j.aquaculture.2020.735148] 19. Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X. and Rozas, R., 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18), 2496-2497. Doi: 10.1093/bioinformatics/btg359 [ DOI:10.1093/bioinformatics/btg359] [ PMID] 20. Sanger, F., Nicklen, S. and Coulson, A.R., 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74(12), 5463-5467. Doi: 10.1073/pnas.74.12.5463 [ DOI:10.1073/pnas.74.12.5463] [ PMID] [ PMCID] 21. Shahrani, K.F., Sourinejad, I., Tamadoni, J.S. and Akbarzadeh, A., 2015. Genetic diversity of jinga shrimp Metapenaeus affinis in the Persian gulf based on mitochondrial gene 16S rRNA sequencing. 22. Simon, C., Franke, A. and Martin, A., 1991. The Polymerase Chain Reaction: DNA Extraction and Amplification. In Molecular Techniques in Taxonomy (pp. 329-355). Berlin, Heidelberg: Springer Berlin Heidelberg. Doi: 10.1007/978-3-642-83962-7_22 [ DOI:10.1007/978-3-642-83962-7_22] 23. Soares, P.E.T., Dantas, M.D.A., de Cássia, B., Silva-Portela, R., Agnez-Lima, L.F. and Lanza, D.C.F., 2021. Characterization of Penaeus vannamei mitogenome focusing on genetic diversity. PLOS ONE, 16(7), e0255291. Doi: 10.1371/JOURNAL.PONE.0255291 [ DOI:10.1371/journal.pone.0255291] [ PMID] [ PMCID] 24. Sourinejad, I., Keshavarzi, F., Tamadoni Jahromi, S. and Vahidinejad, S., 2014. Primary study of phylogeny and genetic structure of Banana shrimp Fenneropenaeus merguiensis in Laft and Sirik estuaries in the Persian Gulf using mitochondrial 16S rRNA gene sequencing. Taxonomy and Biosystematics, 6(20), 23-36. Doi: 20.1001.1.20088906.1393.6.20.4.7 25. Sun, C., Yang, F., Huang, Q., Zeng, X., Zhang, Y., Li, S. and Zhang, Q., 2022. Genetic population structure and demographic history of the endemic fish Paralichthys olivaceus of the Northwest Pacific Ocean. Ecology and Evolution, 12(11), e9506. Doi: 10.1002/ece3.9506 [ DOI:10.1002/ece3.9506] [ PMID] [ PMCID] 26. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S., 2011. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28(10), 2731-2739. Doi: 10.1093/molbev/msr121 [ DOI:10.1093/molbev/msr121] [ PMID] [ PMCID] 27. Thöny-Meyer, L., Beck, C., Preisig, O. and Hennecke, H., 1994. The ccoNOQP gene cluster codes for a cb-type cytochrome oxidase that functions in aerobic respiration of Rhodobacter capsulatus. Molecular Microbiology, 14(4), 705-716. Doi: 10.1111/j.1365-2958.1994.tb01308.x [ DOI:10.1111/j.1365-2958.1994.tb01308.x] [ PMID] 28. Valles-Jimenez, R., Cruz, P. and Perez-Enriquez, R., 2004. Population Genetic Structure of Pacific White Shrimp (Litopenaeus vannamei) from Mexico to Panama: Microsatellite DNA Variation. Marine Biotechnology 2004 6:5, 6(5), 475-484. Doi: 10.1007/S10126-004-3138-6 [ DOI:10.1007/s10126-004-3138-6] [ PMID] 29. Zardoya, R., Castılho, R., Grande, C., Favre-Krey, L., Caetano, S., Marcato, S. and 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(7), 1785-1798. Doi: 10.1111/j.1365-294X.2004.02198.x [ DOI:10.1111/j.1365-294X.2004.02198.x] [ PMID]
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Pazir M, Dashtiannasab A, Kakoolaki S, Mohammadi E, Pourmozaffar S, Hakiminia I et al . Penaeus vannamei broodstock genetic diversity based on 16S rRNA gene mtDNA. injbir 2023; 1 (1) :1-12 URL: http://injbir.com/article-1-21-en.html
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