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Complete mitochondrial DNA sequence of Persian sturgeon, Acipenser persicus: Mitogenome characterization and phylogenetic implications | ||
| Caspian Journal of Environmental Sciences | ||
| مقالات آماده انتشار، اصلاح شده برای چاپ، انتشار آنلاین از تاریخ 04 اسفند 1403 اصل مقاله (808.68 K) | ||
| نوع مقاله: Research Paper | ||
| شناسه دیجیتال (DOI): 10.22124/cjes.2025.8479 | ||
| نویسندگان | ||
| Shirin Jamshidi1؛ Samira Nazemroaya2؛ Ayeh Sadat Sadr2؛ Maryam Monsef Shokri1؛ Hossein Khara3؛ Mohammad Hassanzadeh Saber1 | ||
| 1International Sturgeon Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organization, Rasht, Iran | ||
| 2South of Iran Aquaculture Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organization, Ahvaz, Iran | ||
| 3Faculty member Islamic Azad University of Lahijan, Lahijan, Iran | ||
| چکیده | ||
| This study aimed to determine the complete mitochondrial genome of the Persian sturgeon. Acipenser persicus, Borodin 1897 by direct sequencing of PCR products to understand the systematic status of this species. The whole mitogenome sequence has been deposited in GenBank under accession number MW713795. The circular mitochondrial genome was 16,588 bp long and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region (D-loop). Besides, all genes were encoded on the heavy strain except for ND6 and eight tRNA genes, exhibiting high similarity with other vertebrates in mitochondrial gene arrangement. The overall nucleotide composition was 30.30 % A (a: 5026), 29.17 % C (c: 4839), 16.30 % G (g: 2702), 24.23 % T (4020: t), and a degenerate nucleotide (R), with a skewness of 55.5 % AT. This research characterized the termination-associated sequence domain (ETAS), two central conserved sequence block domains (CSB-E and CSB-F), and three conserved sequence block domains (CSB-1, CSB-2, and CSB-3) in the control region. It corroborates the regulatory elements of the D-loop, indicating similarities across the sturgeon control region to that of other fish, showing the homologous of the CSB-conserved blocks located upstream of these blocks. Moreover, results further supported the Persian sturgeon evolution by phylogenetic tree based on encoded H-strand 13 protein-coding genes of mitochondrial genomes of 23 related species. The results indicated that A. persicus is closely related to Acipenser gueldenstaedtii and forms a monophyletic group with Acipenser sinensis. | ||
| کلیدواژه‌ها | ||
| Acipenser persicus؛ Persian sturgeon؛ mitochondrial genome؛ phylogenetic | ||
| مراجع | ||
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Adeli, A & Namdar, M 2015, The Iranian Caviar and its substitutes in the world market. Ecopersia, 3: 933-944.
Alzohairy, AM 2011, BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences, 2: 60-61.
Bailey, TL, Boden, M, Buske, FA, Frith, M, Grant, CE, Clementi, L, Ren, J, Li, WW & Noble, WS 2009, MEME SUITE: tools for motif discovery and searching Nucleic Acids Research, vol. 37 (Web Server issue), pp. 202-208. DOI: https://doi.org/10.1093/nar/gkp335.
Boore, JL 1999, Animal mitochondrial genomes, Nucleic Acids Research, 27: 1767-1780. DOI: https://doi.org/ 10.1093/nar/27.8.1767.
Chen, CA, Ablan, MCA, McManus, JW, Bell, JD, Tuan, VS, Cabanban, AS & Shao, KT 2004, Variable numbers of tandem repeats (VNTRs), heteroplasmy, and sequence variation of the mitochondrial control region in the threespot Dascyllus, Dascyllus trimaculatus (Perciformes: Pomacentridae). Zoological Studies, 43: 803-812.
Chen, DX, Chu, WY, Liu, XL, Nong, XX, Li, YL, Du, SJ & Zhang, JS 2012, Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences. Mitochondrial DNA, 23: 70-76. DOI: https://doi.org/10.3109/19401736.2011.653799.
Chu, W, Chen, D, Wang, K, Li, Y, Du, S & Zhang, J 2013, Analysis of the variable sites and phylogenetic studies of complete mitochondrial DNA based on the Siniperca scherzeri (Perciformes: Sinipercidae) from four different areas. Mitochondrial DNA, 24: 288-289. DOI: https://doi.org/10.3109/19401736.2012.748042.
Dadkhah, K, Rahimi, G & Farhadi, A 2019, Analysis of complete structure of mitochondrial D-loop region with regulating motifs in four sturgeon species of the Caspian Sea. Iranian Scientific Fisheries Journal, 28: 13-23. DOI: https://doi.org/10.22092/ISFJ.2019.119488.
Dong, C, Chen, B, Xu, J, Mahboob, S, Al-Ghanim, K, Xu, P & Sun, X 2016, The complete mitochondrial genome of Russian sturgeon (Acipenser gueldenstaedtii). Mitochondrial DNA Part A, 27: 986-987. DOI: https://doi.org/10.3109/19401736.2014.926517.
Friedrich, T, Reinartz, R & Gessner, J 2019, Sturgeon re-introduction in the Upper and Middle Danube River Basin. Journal of Applied Ichthyology, 35: 1059-1068. DOI: https://doi.org/10.1111/jai.13966.
Hall, T, Biosciences, I & Carlsbad, C 1999, BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series, 41: 95-98.
Inoue, JG, Kumazawa, Y, Miya, M & Nishida, M 2009, The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Molecular Phylogenetics and Evolution, 51: 486-499, DOI: https://doi.org/10.1016/ j.ympev.2009.01.020.
Islam, M N, Sultana, S & Alam, MJ 2020, Sequencing and annotation of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba. Genomics & Informatics, 18: 32, DOI: https://doi.org/ 10.5808/GI.2020.18.3.e32.
Kottelat, M & Freyhof, J 2007, Handbook of European freshwater fishes. CF Kottelat (ed), Kottelat, Cornol & Freyhof, Berlin, Germany.
Krieger, J, Hett, AK, Fuerst, PA, Artyukhin, E & Ludwig, A 2008, The molecular phylogeny of the order Acipenseriformes revisited. Journal of Applied Ichthyology, 24: 36-45, DOI: https://doi.org/10.1111/j.1439-0426.2008.01088.x.
Kumar, S, Stecher, G, Li, M, Knyaz, C & Tamura, K 2018, MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35: 1547-1549. DOI: https://doi.org/10.1093/ molbev/msy096.
Lee, WJ, Conroy, J, Howell, WH & Kocher, TD 1995, Structure and evolution of teleost mitochondrial control regions. Journal of Molecular Evolution, 41: 54-66, DOI: https://doi.org/10.1007/BF00174041.
Lee, YS, Oh, J, Kim, YU, Kim, N, Yang, S & Hwang, UW 2007, Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. Nucleic Acids Research, 36: D938-D942. DOI:https://doi.org/10.1093/nar/gkm763.
Li, C, Cheng, L, Li, JT, Lu, CY, Wang, Y & Sun, XW 2015, Complete mitochondrial genome of sterlet (Acipenser ruthenus). Mitochondrial DNA, 26: 259-260. DOI: https://doi.org/10.3109/19401736.2013.823188.
Li, C, Lu, CY, Li, JT, Cheng, L, Zheng, XH & Sun, X W 2014, Complete mitochondrial genome of Amur sturgeon (Acipenser schrenckii). Mitochondrial DNA, 25: 282-283. DOI: https//doi.org/10.3109/19401736. 2013.800507.
Liao, X, Tian, H, Zhu, B & Chang, J 2016, The complete mitochondrial genome of Chinese sturgeon (Acipenser sinensis). Mitochondrial DNA Part A, 27: 328-329, DOI: https://doi.org/10.3109/19401736.2014.892101.
Liu, J, Tan, C, Xiao, K, Wang, B, Liu, X & Du, H 2017, The complete mitochondrial genome of Dabry’s sturgeon (Acipenser dabryanus). Mitochondrial DNA Part B, 2: 54-55. DOI: https://doi.org/10.1080/23802359.2017. 1280698.
Lu, C, Gu, Y, Li, C, Cheng, L & Sun, X 2016, The complete mitochondrial genome of Endangered fish Huso dauricus (Acipenseriformes: Acipenseridae). Mitochondrial DNA Part A, 27: 395-396. DOI: https://doi.org/ 10.3109/19401736.2014.896002.
Miya, M, Takeshima, H, Endo, H, Ishiguro, NB, Inoue, JG, Mukai, T, Satoh, TP, Yamaguchi, M, Kawaguchi, A, Mabuchi, K, Shirai, SM, Nishida, M 2003, Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences Molecular Phylogenetics and Evolution, 26: 121-138. DOI: https://doi.org/10.1016/S1055-7903(02)00332-9.
Nejat, SA, Hermidas Bavand, D & Farshchi, P 2018, Environmental challenges in the Caspian Sea and international responsibility of its littoral states. Caspian Journal of Environmental Sciences, 16: 97-110, DOI: https://doi.org/10.22124/cjes.2018.2953.
Ortí, G, Sivasundar, A, Dietz, K & Jégu, M 2008, Phylogeny of the Serrasalmidae (Characiformes) based on mitochondrial DNA sequences. Genetics and Molecular Biology, 31: 343-351, DOI: https://doi.org/10.1590/ S1415-47572008000200030.
Rastorguev, S, Mugue, N, Volkov, A & Barmintsev, V 2008, Complete mitochondrial DNA sequence analysis of Ponto-Caspian sturgeon species. Journal of Applied Ichthyology, 24: 46-49. DOI: https://doi.org/10.1111/ j.1439-0426.2008.01089.x.
Rocha-Reis, DA, Pasa, R, Menegidio, FB, Heslop-Harrison, JS, Schwarzacher, T & Kavalco, KF 2020, The complete mitochondrial genome of two armored catfish populations of the genus Hypostomus (Siluriformes, Loricariidae, Hypostominae). Frontiers in Ecology and Evolution, 8: 579965. DOI: https://doi.org/10.3389/ fevo.2020.579965.
Saccone, C, Pesole, G & Sbisá, E 1991, The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern. Journal of Molecular Evolution, 33: 83-91, DOI: https:// doi.org/10.1007/BF02100199.
Sanger, F, Nicklen, S & Coulson, AR 1977, DNA sequencing with chain-terminating inhibitors, Proceedings of the National Academy of Sciences, 74: 5463-5467. DOI: https://doi.org/10.1073/pnas.74.12.5463.
Sato, Y, Miya, M, Fukunaga, T, Sado, T & Iwasaki, W 2018, MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding, Molecular Biology and Evolution, vol. 35, no. 6, pp. 1553-1555. DOI: https://doi.org/10.1093/molbev/msy074.
Sbisà, E, Tanzariello, F, Reyes, A, Pesole, G & Saccone, C 1997, Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications, Gene, 205: 125-140. DOI: https://doi.org/10.1016/S0378-1119(97)00404-6.
Shadel, GS & Clayton, DA 1997, Mitochondrial DNA maintenance in vertebrates. Annual Review of Biochemistry, 66: 409-435. DOI: https://doi.org/10.1146/ANNUREV.BIOCHEM.66.1.409.
Sheraliev, B & Peng, Z 2020, Complete mitochondrial genome sequence and phylogenetic position of the Amu Darya sturgeon, Pseudoscaphirhynchus kaufmanni (Acipenseriformes: Acipenseridae), Journal of Applied Ichthyology, 36: 389-392, DOI: https://doi.org/10.1111/jai.14043.
Tavakoli, M, Behrooz Khoshghalb, MR, Kor, D & Ghadirnejad, H 2017, Stock assessment of juvenile sturgeons in the Iranian water of the Caspian Sea by bottom trawl survey. Caspian Journal of Environmental Sciences, 15: 147-156, DOI: https://doi.org/10.22124/cjes.2017.2371.
Terencio, ML, Schneider, CH, Gross, MC, Feldberg, E & Porto, JIR 2013, Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish. Mitochondrial DNA, 24: 74-82, DOI: https://doi.org/10.3109/19401736.2012.717934.
Wang, H, Zhang, B, Li, L & Chen, J 2015, The complete mitochondrial genome of the Acipenser schrenckii (Acipenseridae: Acipenser). Mitochondrial DNA, 26: 137-138. DOI: https://doi.org/10.3109/19401736.2013. 815174.
Yang, L, Tan, Z, Wang, D, Xue, L, Guan, M x, Huang, T & Li, R 2014, Species identification through mitochondrial rRNA genetic analysis. Scientific Reports, 4: 1-11, DOI: https://doi.org/10.1038/srep04089.
Zhang, WZ, Xiong, XM, Zhang, XJ, Wan, SM, Guan, NN, Nie, CH, Zhao, BW, Hsiao, CD, Wang, WM, Gao, ZX 2016, Mitochondrial genome variation after hybridization and differences in the first and second generation hybrids of bream fishes, PloS One, 11: e0158915. DOI: https://doi.org/10.1371/journal.pone.0158915.
Zhuang, X, Qu, M, Zhang, X & Ding, S 2013, A comprehensive description and evolutionary analysis of 22 grouper (Perciformes, Epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PloS One, 8: e73561. DOI: https://doi.org/10.1371/journal.pone.0073561. | ||
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