Cite this paper:
CAO Liang, SONG Xuelin, ZHANG E. The first mitogenome of the Nile pufferfish Tetraodon lineatus from Lake Turkana in East Africa: new insights into the genus[J]. HaiyangYuHuZhao, 2020, 38(2): 490-502

The first mitogenome of the Nile pufferfish Tetraodon lineatus from Lake Turkana in East Africa: new insights into the genus

CAO Liang1,3, SONG Xuelin1,2, ZHANG E1,3
1 Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China;
3 Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
Abstract:
A complete mitogenome of T. lineatus from Lake Turkana in the Kenyan part was determined. It had a length of 16 470 bp, including 37 genes as found in teleosts with the typical gene order in these fishes. Mitogenomic comparison and phylogenetic analysis supported not only the morphology-based recognition of the pufferfish specimen from Lake Turkana as the Nile pufferfish, but also the identification of the Chinese specimen recently recorded as T. lineatus and its African source. The mitochondrial genome here amplified for the sample of T. lineatus from Lake Turkana also provides conclusive molecular evidence for the monophyletic nature of Tetraodon s.s., as it serves as a reference genome of this species used to clarify ambiguity in its identification in previous molecular studies.
Key words:    Tetraodon lineatus|Kenya|mtDNA|phylogenetic analysis   
Received: 2019-03-06   Revised: 2019-04-28
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References:
Bibb M J, Van Etten R A, Wright C T, Walberg M W, Clayton D A. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell, 26(2):167-180.
Brainerd E L. 1994. Pufferfish inflation:functional morphology of postcranial structures in Diodon holocanthus(Tetraodontiformes). Journal of Morphology, 220(3):243-261.
Brenner S, Elgar G, Sanford R, Macrae A, Venkatesh B, Aparicio S. 1993. Characterization of the pufferfish(Fugu) genome as a compact model vertebrate genome.Nature, 366(6452):265-268.
Crnogorac-Jurcevic T, Brown J R, Lehrach H, Schalkwyk L C. 1997. Tetraodon fluviatilis, a new puffer fish model for genome studies. Genomics, 41(2):177-184.
Dekkers W J. 1975. Review of the Asiatic freshwater puffers of the genus Tetraodon Linnaeus, 1758 (Pisces, Tetraodontiformes, Tetraodontidae). Bijdragen tot de Dierkunde, 45(1):87-142.
Deraniyagala P E P. 1948. Some scientific results of two visits to Africa Spolia. Zeylanica, 25:1-42.Ebert K. 2001. The Puffers of Fresh and Brackish Waters.Aqualog verlag GmbH, Rodgau, Germany. 96p.
Feibel C S. 2011. A geological history of the Turkana basin.Evolutionary Anthropology:Issues, News, and Reviews, 20(6):206-216.
Gong X L, Zhang Q, Bao B L. 2016. Complete mitochondrial DNA sequence of globe fish Tetraodon lineatus (Linnaeus, 1758) and the phylogenetic analysis of Tetraodontidae.Mitochondrial DNA Part B, 1(2):781-782.
Habteselassie R D. 2012. Fishes of Ethiopia:annotated checklist with pictorial identification guide. Ethiopian Fisheries and Aquatic Science Association, Addis Ababa, Ethiopia. 250p.
Hamblyn E. 1962. A note on Lake Rudolf East. African Freshwater Fisheries Research Organization Annual Report, 1961. p.46-47.
Hardman M. 2008. A new species of Chrysichthys(Siluriformes:Claroteidae) from Lake Turkana, Kenya.Proceedings of the Academy of Natural Sciences of Philadelphia, 157(1):25-36.
Hinegardner R, Rosen D E. 1972. Cellular DNA content and the evolution of teleostean fishes. The American Naturalist, 106(951):621-644.
Hopson A J, Hopson J. 1982. The fishes of Lake Turkana with a description of three new species:Alestes ferox sp. nov., Alestes minutus sp. nov. (Pisces, Characidae) and Barbus turkanae sp. nov. (Pisces, Cyprinidae). In:Hopson A J ed.Lake Turkana. Overseas Development Administration, London, England. p.283-347.
Igarashi Y, Doi H, Yamanoue Y, Kinoshita S, Ishibashi T, Ushio H, Asakawa S, Nishida M, Watabe S. 2013.Molecular phylogenetic relationship of Tetraodon pufferfish based on mitochondrial DNA analysis. Fisheries Science, 79(2):243-250.
Kartavtsev Y P, Jung S O, Lee Y M, Byeon H K, Lee J S. 2007.Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae):Genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene, 396(1):13-27.
Katoh K, Misawa K, Kuma K I, Miyata T. 2002. MAFFT:a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14):3 059-3 066.
Kottelat M. 2013. The fishes of the inland waters of southeast Asia:a catalogue and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries.The Raffles Bulletin of Zoology, (S27):1-663.
Lalitha S. 2000. Primer premier 5. Biotech Software & Internet Report, 1(6):270-272.
Lanfear R, Calcott B, Ho S Y W, Guindon S. 2012.PartitionFinder:combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6):1 695-1 701.
Lévêque C. 1992. Tetraodontidae. In:Lévêque C, Paugy D, Teugels G G eds. The Fresh and Brackish Water Fishes of West Africa:Volume 2. Collection Faune Tropicale 28.MRAC, Tervuren, Belgique and ORSTOM, Paris, France.p.868-870.
Li Z Q, Guo B C, Li J B, He S P, Chen Y Y. 2008. Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae:Sinocyclocheilus). Chinese Science Bulletin, 53(15):2 342-2 352.
Liang S H, Chuang L C, Chang M H. 2006. The pet trade as a source of invasive fish in Taiwan. Taiwania, 51(2):93-98
Lo Y M. 1998. Clinical Applications of PCR. Humana Press, Totowa, New Jersey, USA. 326p.
Mann M 1964. Report on A Fisheries Survey of Lake Rudolf, Kenya. Government printer, Nairobi, Kenya. Annual Report 1962/63:53-62, East African Freshwater Fisheries Research Organization.
Mohammed-Geba K, Mahdy A A, Eissa A S A, Osman A G M. 2016. Analysis of population genetics of the endangered Nile pufferfish Tetraodon lineatus (Linnaeus, 1758) in the upper Egyptian River Nile. International Journal of Ecotoxicology and Ecobiology, 1(2):60-66.
Nelson J S. 2006. Fishes of the world. John Wiley and Sons, New Jersey, USA. 601p.
Nyingi W D. 2013. Guide to Common Freshwater Fishes of Kenya. Moran Publishers, Nairobi, Kenya. 136p.
Peng Z G, Wang J, He S P. 2006. The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius(Siluriformes:Cranoglanididae) and the phylogeny of otophysan fishes. Gene, 376(2):290-297.
Roberts T R. 1975. Geographical distribution of African freshwater fishes. Zoological Journal of the Linnean Society, 57(4):249-319.
Santini F, Nguyen M T T, Sorenson L, Waltzek T B, Alfaro J W L, Eastman J M, Alfaro M E. 2013. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae). Journal of Evolutionary Biology, 26(5):1 003-1 018.
Seegers L, De Vos L, Okeyo D O. 2003. Annotated checklist of the freshwater fishes of Kenya (excluding the lacustrine haplochromines from Lake Victoria). Journal of East African Natural History, 92(1):11-47.
Silvestro D, Michalak I. 2012. raxmlGUI:a graphical frontend for RAxML. Organisms Diversity & Evolution, 12(4):335-337.
Singh V K, Mangalam A K, Dwivedi S, Naik S. 1998. Primer premier:program for design of degenerate primers from a protein sequence. Biotechniques, 24(2):318-319.
Tyler J C. 1980. Osteology, Phylogeny, and Higher Classification of the Fishes of the Order Plectognathi(Tetraodontiformes). NOAA Technical Report NMFS Circular 434, NOAA, Washington DC, America. p.1-422.
Wakjira M, Getahun A. 2017. Ichthyofaunal diversity of the Omo-Turkana basin, East Africa, with specific reference to fish diversity within the limits of Ethiopian waters.Check List, 13(2):2 059.
Wang J J, Li P, Zhang Y G, Peng Z G. 2011a. The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei:Cypriniformes).Mitochondrial DNA, 22(5-6):178-180.
Wang Y, Guo R, Li H, Zhang X Y, Du J, Song Z B. 2011b. The complete mitochondrial genome of the Sichuan taimen(Hucho bleekeri):repetitive sequences in the control region and phylogenetic implications for Salmonidae.Marine Genomics, 4(3):221-228.
Xia X, Xie Z. 2001. DAMBE:software package for data analysis in molecular biology and evolution. Journal of Heredity, 92(4):371-373.
Xiong W, Sui X Y, Liang S H, Chen Y F. 2015. Non-native freshwater fish species in China. Reviews in Fish Biology and Fisheries, 25(4):651-687.
Yamanoue Y, Miya M, Doi H, Mabuchi K, Sakai H, Nishida M. 2011. Multiple invasions into freshwater by pufferfishes (Teleostei:Tetraodontidae):a mitogenomic perspective. PLoS One, 6(2):e17410.
Yamanoue Y, Miya M, Inoue J G, Matsuura K, Nishida M. 2006. The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei:Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes & Genetic Systems, 81(1):29-39.
Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, Nishida M. 2004. Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes:Molidae).Ichthyological Research, 51(3):269-273.
Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, Nishida M. 2008. A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces:Acanthopterygii) based on whole mitochondrial genome sequences:Basal ecological diversification? BMC Evolutionary Biology, 8:212.
Yamanoue Y, Miya M, Matsuura K, Miyazawa S, Tsukamoto N, Doi H, Takahashi H, Mabuchi K, Nishida M, Sakai H. 2009. Explosive speciation of Takifugu:another use of fugu as a model system for evolutionary biology.Molecular Biology and Evolution, 26(3):623-629.
Yamanoue Y, Miya M, Matsuura K, Yagishita N, Mabuchi K, Sakai H, Katoh M, Nishida M. 2007. Phylogenetic position of tetraodontiform fishes within the higher teleosts:Bayesian inferences based on 44 whole mitochondrial genome sequences. Molecular Phylogenetics and Evolution, 45(1):89-101.
Yu J N, Kwak M. 2015. The complete mitochondrial genome of Brachymystax lenok tsinlingensis (Salmoninae, Salmonidae) and its intraspecific variation. Gene, 573(2):246-253.
Zhang C G, Zhao Y H, Xing Y C, Zhou W, Tan, W Q. 2016.Species Diversity and Distribution of Inland Fishes in China. Science Press, Beijing. 284p. (in Chinese with English abstract)
Zhou L W, Feng Y, Wang G F, Wu N H. 1993. Structure analysis of the mitochondrial tRNA(Cys) gene and the original region of light-strand replication from carp. Acta Biologiae Experimentalis Sinica, 26(4):463-468. (in Chinese with English abstract)