Percent identity and phylogenetic relationships of Caspian Sea sturgeon species based on mitochondrial genome sequences

Document Type : Research Paper

Authors

1 International Sturgeon Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran

2 Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran

10.22059/jfisheries.2023.358558.1384

Abstract

Mitochondrial genome is an ideal model to study evolution and phylogenetic relationships. In this study, complete mitochondrial genomes of six species of Caspian sea sturgeon including Persian sturgeon, Russian sturgeon, Ship sturgeon, Sterlet sturgeon, Starry sturgeon and Beluga sturgeon along with separate nucleotide and amino acid sequences of 13 PCGs per each genome including ND1, ND2, ND3, ND4, ND5, ND6, ATP6, ATP8, COX1, COX2, COX3, ND4L and CYTB were retrieved from NCBI database and compared. The results obtained from sequence distance analysis by DNAStar software based on complete mitochondrion genome showed high genetic similarity (99 %) between Persian and Russian sturgeon. Also, the lowest similarity (95 %) was observed between Sterlet and Starry sturgeon. In phylogenetic analysis by MEGA7 software, two main clusters with two sub-clusters for one of the main clusters were identified. Persian and Russian sturgeon species were grouped in first sub-cluster, Ship and Sterlet species fall in the other sub-cluster and Starry sturgeon with Beluga formed a different distinct cluster. The results obtained from the comparison of the 13 PCGs sequences were similar to the sequences of the complete mitochondrial genomes. The most difference in nucleotide sequences were observed in CYTB, ATP6, ND2, ND5 and ND6 genes and the lowest difference for ND4L gene. The results obtained from the comparison of the 13 genes amino acid sequences were different as the order of the species was changed and 100 % genetic similarity were observed for some genes such as COX3 and ND4L genes. Based on the results of the present study, mitochondrial genome sequences could be used for phylogenetic analysis and clustering of different species of sturgeons. However, the accuracy of investigations by complete mitochondrial genomes is higher than the nucleotide sequences of the genes, and using the amino acid sequences is not suggested due to their codon nature.

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Main Subjects


Abdoli, R., Mazumder, T.H., Nematollahian, S., Sourati Zanjani, R., Abdolahi Mesbah, R., 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
Abdoli, R., Zamani, P., Ghasemi, M., 2018. Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences. Meta Gene 15, 23-26. DOI: 10.1016/j.mgene.2017.10.004
Ariaeenejad, S., Kavousi, K., Elahi, E., Banaei-Moghaddam, A.M., Moosavi-Movahedi, A.A., 2022. Sturgeons: An Evolutionary Insight to The α-globin Protein Speciation and Diversification. bioRxiv 2022-06. DOI: 10.1101/2022.06.11.495750
Artyukhin, E.N., 2010. Morphological phylogeny of the order Acipenseriformes. Journal of Applied Ichthyology 22(1), 66-69. DOI: 10.1111/j.1439-0426.2007.00930.x
Avise, J.C., Bowen, B.W., Lamb, T., Meylan, A.B., Bermingham, E. 1992. Mitochondrial DNA evolution at a turtle's pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines. Molecular Biology and Evolution 9(3), 457-473. DOI: 10.1093/oxfordjournals.molbev.a040735
Behura, S.K., 2015. Insect phylogenomics. Insect Molecular Biology 24(4), 403-411. DOI: 10.1111/imb.12174
Bemis, W.E., Kynard, B., 1997. Sturgeon rivers: An introduction to Acipenseriformes biogeography and life history. Environmental Biology of Fishes 48, 167-183. DOI: https://doi.org/10.1023/A:1007312524792
Boore, J.L., 1999. Animal mitochondrial genomes. Nucleic Acids Research 27(8), 1767-1780. DOI: 10.1093/nar/27.8.1767
Brown, W.M., George, M., Wilson, A.C., 1979. Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America 76(4), 1967-1971. DOI: 10.1073/pnas.76.4.1967
Choudhury, A., Dick, T.A., 1998: The historical biogeography of sturgeons (Osteichthyes: Acipenseridae): a synthesis of phylogenetics, palaeontology and palaeogeography. Journal of Biogeography 25(4), 623-640. DOI: 10.1046/j.1365-2699.1998.2540623.x
Cieslak, M., Pruvost, M., Benecke, N., Hofreiter, M., Morales, A., Reissmann, M., Ludwig, A., 2010. Origin and history of mitochondrial DNA lineages in domestic horses. PLoS One 5(12), e15311. DOI: 10.1371/journal.pone.0015311
Comber, S.C.L., Smith, C., 2004. Polyploidy in fishes: patterns and processes. Biological Journal of the Linnean Society 82(4), 431-442. DOI: 10.1111/j.1095-8312.2004.00330.x
‏da Silva, F.S., Cruz, A.C.R., de Almeida Medeiros, D.B., 2020. Mitochondrial genome sequencing and phylogeny of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis (Diptera: Culicidae). Scientific Reports 10(1), 16948. DOI: 10.1038/s41598-020-73790-x
Dos Reis, M., Donoghue, P.C.J., Yang, Z., 2015. Bayesian molecular clock dating of species divergences in 529 the genomics era. Nature Reviews Genetics 17(2), 71-80. DOI: 10.1038/nrg.2015.8
Fontana, F., Tagliavini, J., Congiu, L., 2001. Sturgeon genetics and cytogenetics: Recent advancements and perspectives. Genetica 111, 359-373. DOI: 10.1023/A:1013711919443
Harrison, R.G., 1989. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends in Ecology & Evolution 4(1), 6-11. DOI: 10.1016/0169-5347(89)90006-2
Khoshkholgh, M., Pourkazemi, M., Nazari, S., Azizzadeh Pormehr, L., 2011. Genetic diversity in the Persian sturgeon, Acipenser percicus, from the south Caspian Sea based on mitochondrial DNA sequences of the control region. Caspian Journal of Environmental Sciences 9(1), 17-25.  
Krieger, J., Fuerst, P.A., 2002. Evidence for a slowed rate of molecular evolution in the order Acipenseriformes. Molecular Biology Evolution 19(6), 891-897. DOI: 10.1093/oxfordjournals.molbev.a004146
Luo, D., Li, Y., Zhao, Q., Zhao, L., Ludwig, A., Peng, Z., 2019. Highly resolved phylogenetic relationships within order Acipenseriformes according to novel nuclear markers. Genes 10(1), 38. DOI: 10.3390/genes10010038
Martin, A.P., 1999. Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again). Molecular Biology Evolution 16(7), 996-1002. DOI: 10.1093/oxfordjournals.molbev.a026189
Martin, A.P., Naylor, G.J., Palumbi, S.R., 1992. Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357(6374), 153-155. DOI: https://doi.org/10.1038/357153a0
Martin, A.P., Palumbi, S.R., 1993. Body size, metabolic rate, generation time, and the molecular clock. Proceedings of the National Academy of Sciences 90(9), 4087-4091. DOI: 10.1073/pnas.90.9.4087
Miuge, N.S., Barmintseva, A.E., Rastorguev, S.M., Miuge, V.N., Barmintsev, V.A., 2008. Polymorphism of the mitochondrial DNA control region in eight sturgeon species and development of a system for DNA-based species identification. Genetika 44(7), 913-919. DOI: 10.1134/S1022795408070065
Nazari, S., Pourkazemi, M., Khoshkholgh, M., 2020. Analysis of the genetic structure of the Persian sturgeon (Acipenser persicus) populations: Comparison of control region sequencing and PCR-RFLP analysis of mitochondrial DNA. Iranian Journal of Fisheries Sciences 19(6), 3201-3220.
Peng, Z., Ludwig, A., Wang, D., Diogo, R., Wei, Q., He, S. 2007. Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes). Molecular Phylogenetics and Evolution 42(3), 854-862. DOI: 10.1016/j.ympev.2006.09.008
Pourkazemi, M., 1996. Molecular and biochemical genetic analysis of sturgeon stocks from the South Caspian Sea. Ph.D. thesis. University of Wales, Swansea, UK.
Pramod, R.K., Velayutham, D., Sajesh, P.K., Beena, P.S., Zachariah, A., Zachariah, A., Chandramohan, B., Sujith, S.S., Santhosh, S., Iype, S., Ganapathi, P., Kumar, B.D., Gupta, R., Thomas, G., 2018. The complete mitochondrial genome of Indian cattle (Bos indicus). Mitochondrial DNA B 3(1), 207-208. DOI:   10.1080/23802359.2018.1437836
Rabiei, F., Abdoli, R., Rafiee, F., Ghavi Hossein-Zadeh, N., 2022. Genetic similarities and phylogenetic 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
Rahmani, H., Kazemi, B., Pourkazemi, M., 2012. Comparison of genetic diversity of cytochrome B gene of Shemaya (Alburnus Chalcoides) In Haraz, Shirud and Gazafrud rivers by PCR-RFLP method. Modern Genetics Journal 7(3), 227-232. (in Persian)
Rastorguev, S., Mugue, N., Volkov, A., Barmintsev, V., 2008. Complete mitochondrial DNA sequence analysis of Ponto-Caspian sturgeon species. Journal of Applied Ichthyology, 24(1), 46- 49. DOI: 10.1111/j.1439-0426.2008.01089.x
Rezvani Gilkolaei, S., 1997. Molecular population genetic studies of sturgeon species in the South Caspian Sea. Ph.D. thesis. University of Wales, Swansea, UK.
Rothfels, C.J., Larsson, A., Li, F.W., Sigel, E.M., Huiet, L., Burge, D.O., Ruhsam, M., Graham, S.W., Stevenson, D.W., Wong, G.K., Korall, P., Pryer, K.M., 2013. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS ONE 8(10), e76957. DOI: 10.1371/journal.pone.0076957
Shen, Y., Yang, N., Liu, Z., Chen, Q., Li, Y., 2020. Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes. Genomics 112(5), 3511-3517. DOI: 10.1016/j.ygeno.2020.02.017
Simon, C., Frati, B.F., Stewart, J.B., Beckenbach, A.T., 2006. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 37, 545-579. DOI: 10.1146/annurev.ecolsys.37.091305.110018
Soltis, D.E., Soltis, P.S., 1999. Polyploidy: recurrent formation and genome evolution. Trends in Ecology & Evolution 14(9), 348-352. DOI: 10.1016/S0169-5347(99)01638-9
Tagliavini, J., Conterio, F., Gandolf, G., Fontana, F., 1999. Mitochondrial DNA sequences of six sturgeon species and phylogenetic relationships within Acipenseridae. Journal of Applied Ichthyology 15(4‐5), 17-22. DOI: 10.1111/j.1439-0426.1999.tb00198.x
Tamura, k., Stecher, G., Peterson, D., Filipski, A., Kumar, S., 2016. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology Evolution 30(12), 2725-2729. DOI: 10.1093/molbev/mst197
Townsend, T., Alegre, R., Kelley, S., Wiens, J., Reeder, T.W., 2008. Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles. Molecular Phylogenetics and Evolution 47(1), 129-142. DOI: 10.1016/j.ympev.2008.01.008
Zeng, L., Zhang, N., Zhang, Q., Endress, P.K., Huang, J., Ma, H., 2017. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytologist 214(3), 1338-1354. DOI: 10.1111/nph.14503
Zhang, X., Wu, W., Li, L., Ma, X., Chen, J., 2013. Genetic variation and relationships of seven sturgeon species and ten interspecific hybrids. Genetics Selection Evolution 45(1), 21. DOI: 10.1186/1297-9686-45-21