Study of genetic similarities and phylogenetic relationships of 10 Penaeidae shrimp species based on the sequences of the mitochondrial genome

Document Type : Research Paper

Authors

1 Assistant Professor in Department of Aquatic Health and Diseases, Iranian Shrimp Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Bushehr, Iran

2 Assistant Professor in Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Guilan, Iran

10.22124/japb.2023.24411.1494

Abstract

Penaeidae shrimp species are the most important farmed aquatic animals from the crustacean group which have gained an important economic position in the world's aquaculture industry. In this study, complete mitochondrial genome sequences along with nucleotide and amino acid sequences of 13 PCGs per each genome from 10 important Penaeidae shrimp species were obtained from NCBI database and compared. According to the complete mitochondrial genome, the highest (88.5%) and lowest (76.4%) genetic similarity was found between Fenneropenaeus indicus and Fenneropenaeus merguiensis, and Metapenaeus ensis and Penaeus monodon, respectively. In phylogenetic analysis of the complete mitochondrial genome, two main clusters were established at the beginning of the phylogenetic tree. Metapenaeus ensis and Metapenaeus affinis were placed in one main cluster and other species in another main cluster. The results of the phylogenetic analysis of the nucleotide and amino acid sequences of the 13 PCGs showed that M. ensis and M. affinis, Litopenaeus stylirostris and Litopenaeus vannamei, and F. merguiensis and F. indicus species were grouped in different clusters, which confirms the results obtained from the comparison of the complete mitochondrial genome. Based on the results, mitochondrial genome sequences could be used for a wide range of detailed phylogenetic and genetic analyzes of different shrimp species.

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Main Subjects

References

Abdoli R., Mazumder T.H., Nematollahian S., Sourati Zanjani R., Abdolahi Mesbah R. and Uddin A. 2022. Gaining insights into the compositional constraints and molecular phylogeny of five silkworms mitochondrial genome. International Journal of Biological Macromolecules, 206: 543–552. doi: 10.1016/j.ijbiomac.2022.02.135
Alfaro-Montoya J., Braga A. and Umana-Castro R. 2019. Research frontiers in penaeid shrimp reproduction: Future trends to improve commercial production. Aquaculture, 503: 70–87. doi: 10.1016/j.aquaculture.2018.12.068
Amelia F., Yustiati A. and Andriani Y. 2021. Review of shrimp (Litopenaeus vannamei (Boone, 1931)) farming in Indonesia: Management operating and development. World Scientific News, 158: 145–158.
Arulmoorthy M.P., Anandajothi E., Vasudevan S. and Suresh E. 2020. Major viral diseases in culturable penaeid shrimps: A review. Aquaculture International, 28: 1939–1967. doi: 10.1007/s104 99-020-00568-3
Atashbar B., Agh N., Manaffar R., Stappen G.V., Mohamadyari A., Mertens J. and Beladjal L. 2016. Morphometric and preliminary genetic characteristics of Branchinecta orientalis populations from Iran (Crustacea: Anostraca). Zootaxa, 4109(1): 31–45. doi: 10.11646/zootaxa.4109.1.3
Atashbar B.A. and Roohi M. 2021. First record of Branchipodopsis affinis Sars, 1901 (Crustacea: Anostraca) in Iran (Bazargan, West Azerbaijan), ecology, morphology and genetics. Zootaxa, 4908(4): 558–570. doi: 10.11646/zootaxa.49 08.4.8
Baldwin J.D., Bass A.L., Bowen B.W. and Clark Jr W.H. 1998. Molecular phylogeny and biogeography of the marine shrimp Penaeus. Molecular Phylogenetics and Evolution, 10(3): 399–407. doi: 10.1006/mpev.1998.0537
Burland T.G. 1999. DNASTAR's Lasergene sequence analysis software. Methods in Molecular Biology, 132: 71–91. doi: 10.1385/ 1-59259-192-2:71
Bush S.R., Van Zwieten P.A., Visser L., Van Dijk H., Bosma R., De Boer W.F. and Verdegem M. 2010. Scenarios for resilient shrimp aquaculture in tropical coastal areas. Ecology and Society, 15(2): 1–18. doi: 10.5751/ES-03331-150215
Cheng J., Chan T.Y., Zhang N., Sun S. and Sha Z.L. 2018. Mitochondrial phylogenomics reveals insights into taxonomy   and evolution of Penaeoidea (Crustacea: Decapoda). Zoologica Scripta, 47(5): 1–13. doi: 10.1111/ zsc.12298
Chial H. and Craig J. 2008. mtDNA and Mitochondrial Diseases. Nature Education, 1(1): 217.
Coltman D.W. 2008. Molecular ecological approaches to studying the evolutionary impact of selective harvesting in wildlife. Molecular Ecology, 17(1): 221–235. doi: 10.1111/j.1365-294X.2007. 03414.x
Grabowski M. 1999. Structure and intraspecific variability of the control region mtDNA in the pink shrimp, Farfantepenaeus duorarum (Decapoda, Penaeidae). Crustaceans and the Biodiversity Crisis, 12(5): 333–344. doi: 10.1163/9789004630543_027
Guo Y., Liu H., Feng J., Li J., Ye Y., Guo B. and Qu C. 2021. Characterization of the complete mitochondrial genomes of two species of Penaeidae (Decapoda: Dendrobranchiata) and the phylogenetic implications for Penaeoidea. Genomics, 113(1): 1054–1063. doi: 10.1016/j.ygeno. 2020.11.001
Hurzaid A., Chan T.Y., Nor S.A.M., Muchlisin Z.A. and Chen W.J. 2020. Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from south-east Asian waters. Zoologica Scripta, 49(5): 1–18. doi: 10.1111/ zsc.12428
Iranian Fisheries Organization. 2019. Statistical Yearbook of Iranian Fisheries Organization (In Persian). Deputy Planning and Resource Management, Iranian Fisheries Organization, Iran. 33P.
Katneni V.K., Shekhar M.S., Jangam A.K., Paran B.C., Selvaraj A., Krishnan K. and Koyadan V.K. 2021. Phylogenetic relations and mitogenome‐wide similarity metrics reveal mono-phyly of Penaeus sensu lato. Ecology and Evolution, 11(5): 2040–2049. doi: 10.1002/ece3.7148
Kitaura J., Wada K. and Nishida M. 1998. Molecular phylogeny and evolution of unique mud-using territorial behavior in ocypodid crabs (Crustacea: Brachyura: Ocypodidae). Molecular Biology and Evolution, 15(6): 626–637. doi: 10.1093/oxfordjournals.molbev.a025966
Lavery S., Chan T.Y., Tam Y.K. and Chu K.H. 2004. Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus sp. derived from mitochondrial DNA. Molecular Phylogenetics and Evolution, 31(1): 39–49. doi: 10.1016/j.ympev. 2003.07.015
Ma H., Ma C., Li C., Lu J., Zou X., Gong Y., Wang W., Chen W., Ma L. and Xia L. 2015. First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics. Scientific Reports, 5(1): 1–14. doi: 10.1038/ srep11524
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
Nasvall S.J., Chen P. and Bjork G.R. 2007. The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical for reading of G-ending codons. RNA, 13(12): 2151–2164. doi: 10.1261/rna.731007
Niamaimandi N., Noorinejad M. and Matinfar A. 2009. Biology of Shrimp (In Persian). Publications of Institute of Applied Scientific Higher Education of Jahad Agriculture, Iran. 168P.
Palumbi S.R. and Benzie J. 1991. Large mitochondrial DNA differences between morpho-logically similar penaeid shrimp. Molecular Marine Biology and Biotechnology, 1(1): 27–34.
Quan J., Zhuang Z., Deng J., Dai J. and Zhang Y.P. 2004. Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochemical Genetics, 42: 331–345. doi: 10.1023/B:BIGI. 0000039808.12069.ed
Rabiei F., Abdoli R., Rafeie F. and Ghavi Hossein-Zadeh N. 2022. Genetic similarities and phylo-genetic analysis of wild and domesticated species of sheep based on mitochondrial genome. Animal Production Research, 11(3): 1–13. doi: 10.22124/ar.2022. 22429.1709
Rajakumarana P., Vaseeharana B., Jayakumarb R. and Chidambara R. 2014. Conformation of phylogenetic relationship of Penaeidae shrimp based on morphometric and molecular investigations. Cytology and Genetics, 48: 357–363. doi: 10.3103/S0095452714060103
Robalino J., Wilkins B., Bracken-Grissom H.D., Chan T.Y. and O’Leary M.A. 2016. The origin of large-bodied shrimp that dominate modern global aquaculture. PLoS One, 11(7): 1–24. doi: 10.1371/ journal.pone.0158840
Schubart C.D., Cuesta J.A., Diesel R. and Felder D.L. 2000. Molecular phylogeny, taxonomy, and evolution of nonmarine lineages within the American grapsoid crabs (Crustacea: Brachyura). Molecular Phylogenetics and Evolution, 15(2): 179–190. doi: 10.1006/mpev. 1999.0754
Soares P.E.T., Dantas M.D.A., Silva-Portela R.D.C.B., Agnez-Lima L.F. and Lanza D.C.F. 2021. Characterization of Penaeus vannamei mitogenome focusing on genetic diversity. PLoS One, 16(7): 1–15. doi: 10.1371/journal.pone.0255 291
Stillman J.H. and Reeb C.A. 2001. Molecular phylogeny of eastern Pacific porcelain crabs, genera Petrolisthes and Pachycheles, based on the mtDNA 16S rDNA sequence: Phylogeographic and systematic implications. Molecular Phylogenetics and Evolution, 19(2): 236–245. doi: 10.1006/mpev. 2001.0924
Tamura K., Stecher G. and Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7): 3022–3027. doi: 10.1093/molbev/msab120
Tazikeh E. 2010. Management of Shrimp Farming in Farms (In Persian). Nowruz Press, Iran. 182P.
Zhu P., Luo P., Wang P., Xu Y., Zhang H., Wu H. and Liu L. 2019. The complete mitochondrial genome of Trachypenaeus curvirostris (Stimpson, 1860). Mitochondrial DNA, 4(2): 2834–2835. doi: 10.1080/23802359.2019. 1660279
Aquatic Physiology and Biotechnology
Volume 11, Issue 4
April 2024
Pages 49-81

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