Sains Malaysiana 47(10)(2018): 2519–2531

http://dx.doi.org/10.17576/jsm-2018-4710-29

 

Mitogenome of Gymnothorax minor and Phylogenetic Relationship with Its Congeners and Related Genera (Anguilliformes: Muraenidae)

(Mitogenom Gymnothorax minor dan Hubungan Filogenetik dengan Genus yang Berhubung Kait (Anguilliformes: Muraenidae))

 

SZE-LOOI SONG¹, HOI-SEN YONG², KAR-HOE LOH^1*, PHAIK-EEM LIM¹, AMY YEE-HUI THEN² & PRAPHATHIP EAMSOBHANA³

 

¹Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Federal Territory, Malaysia

 

²Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Federal Territory, Malaysia

 

³Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand

 

Received: 24 January 2018/Accepted: 25 June 2018

 

ABSTRACT

Gymnothorax minor is a moray eel of the family Muraenidae found in the Western Pacific Ocean. We report here its complete mitogenome as determined by Illumina next-generation sequencing and the phylogenetic relationship with its congeners and other taxa of the family Muraenidae. The whole mitogenome of G. minor had a total length of 16,574 bp, comprising 37 genes - 13 protein-coding genes (PCGs), two ribosomal ribonucleic acid (rRNA) and 22 transfer ribonucleic acid (tRNA) genes - and a control region. Excepting cox1 with GTG, the other 12 PCGs had ATG start codon. Seven of its PCGs had incomplete stop codon - five (nad2; cox1; cox2; nad3 and nad4) with T and two (atp6 and cox3) with TA. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes). The subfamily Muraeninae as well as the subfamily Uropterygiinae were monophyletic. However, the genus Gymnothorax was paraphyletic, with G. minor forming a sister group with Rhinomuraena quaesita in the lineage containing also G. kidako and G. formosus forming a sister group with Enchelynassa canina. The phylogenetic relationship of the genus Gymnothorax and related taxa of the family Muraenidae, based on the mitochondrial cob gene, was in general similar to that based on 15 mt-genes. The mitogenome is useful for future studies on phylogenetics and systematics of eels of the family Muraenidae and other taxa of the order Anguilliformes.

 

Keywords: Gymnothorax; mitogenome; moray eels; Muraenidae; next-generation sequencing (NGS)

 

ABSTRAK

Gymnothorax minor adalah belut laut dalam famili Muraenidae yang boleh dijumpai di Lautan Pasifik Barat. Kami melaporkan di sini mitogenom lengkap G. minor yang ditentukan dengan menggunakan penjujukan generasi akan datang Illumina dan hubungan filogenetik G. minor dengan genus yang berhubung kait dan takson yang lain dalam famili Muraenidae. Kepanjangan keseluruhan mitogenom G. minor adalah 16,574 bp yang terdiri daripada 37 gen - 13 gen pengkodan protein (PCGs), dua asid ribonukleik ribosoma (rRNA) dan 22 gen pemindahan ribonukleik ribosoma (tRNA) - dan satu kawasan kawalan. Dua belas PCGs mempunyai kodon pemula ATG kecuali cox1 dengan kodon pemula GTG. Tujuh PCGs mempunyai kodon penamat yang tidak lengkap - lima gen (nad2; cox1; cox2; nad3 dan nad4) dengan T dan dua gen (atp6 dan cox3) dengan TA. Filogeni molekul berdasarkan 13 PCGs adalah konsisten dengan 15 gen mitokondria (13 gen PCGs dan 2 rRNA). Subfamilli Muraeninae dan subfamili Uropterygiinae adalah monofiletik. Walau bagaimanapun, genus Gymnothorax adalah parafiletik dengan G. minor membentuk kumpulan beradik dengan Rhinomuraena quaesita dalam garis keturunan yang mengandungi G. kidako manakala G. formosus membentuk kumpulan beradik dengan Enchelynassa canina. Berdasarkan gen mitokondria cob, hubungan filogenetik genus Gymnothorax dan takson lain dalam famili Muraenidae adalah sama dengan hubungan filogenetik yang berdasarkan 15 gen mitokondria. Mitogenom adalah penting untuk kajian filogenetik dan sistematik belut dalam famili Muraenidae dan takson yang lain dalam order Anguilliformes.

 

Kata kunci: Belut laut; Gymnothorax; mitogenom; Muraenidae; penjujukan generasi akan datang (NGS)

REFERENCES

Alikhan, N.F., Petty, N.K., Ben Zakour, N.L. & Beatson, S.A. 2011. BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genomics 12: 402.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.

Andrews, S. 2010. FastQC: A quality control tool for high throughput sequence data. Available online at: http://www. bioinformatics.babraham.ac.uk/projects/fastqc.

Chen, J.N., Lopez, J.A., Lavoue, S., Miya, M. & Chen, W.J. 2014. Phylogeny of the Elopomorpha (Teleostei): Evidence from six nuclear and mitochondrial markers. Molecular Phylogenetics and Evolution 70: 152-161.

Coluccia, E., Deidda, F., Cannas, R., Lobina, C., Cuccu, D., Deiana, A.M. & Salvadori, S. 2015. Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization. Journal of Fish Biology 87: 634-645.

Du, M., Yin, S.W. & Niu, B.Z. 2016. Phylogenetic relationships of twenty Gymnothorax species based on cytochrome b sequence data. Genetics and Molecular Research 15(2): gmr.15028157.

Ebner, B.C., Kroll, B., Godfrey, P., Thuesen, P.A., Vallance, T., Pusey, B., Allen, G.R., Rayner, T.S. & Pema, C.N. 2011. Is the elusive Gymnothorax polyuranodon really a freshwater moray? Journal of Fish Biology 79: 70-79.

Fishelson, L. 1990. Rhinomuraena spp. (Pisces: Muraenidae): The first vertebrate genus with post-anally situated urogenital organs. Marine Biology 105: 253-257.

Froese, R. & Pauly, D. 2017. FishBase. Accessed through: World Register of Marine Species at http://www.marinespecies.org/ aphia.php?p=taxdetails&id=125636.

Heatwole, H. & Poran, N.S. 1995. Resistances of sympatric and allopatric eels to sea snake venoms. Copeia 1995: 136-147.

Heatwole, H. & Powell, J. 1998. Resistance of eels (Gymnothorax) to the venom of sea kraits (Laticauda colubrina): A test of coevolution. Toxicon 36: 619-625.

Hibino, Y., Nguyen, V.Q. & Kimura, S. 2016. First record of Gymnothorax minor from Vietnam (Anguilliformes: Muraenidae). Journal of Biogeography 18: 63-66.

Inoue, J.G., Miya, M., Miller, M.J., Sado, T., Hanel, R., Hatooka, K., Aoyama, J., Minegishi, Y., Nishida, M. & Tsukamoto, K. 2010. Deep-ocean origin of the freshwater eels. Biology Letters 6: 363-366.

Loh, K.H., Shao, K.T., Chen, H.M., Chen, C.H., Loo, P.L., Then, A.Y.H., Lim, P.E., Chong, V.C., Shen, K.N. & Hsiao, C.D. 2016a. Next-generation sequencing yields the complete mitochondrial genome of the longfang moray, Enchelynassa canina (Anguilliformes: Muraenidae). Mitochondrial DNA Part A, DNA Mapping, Sequencing, and Analysis 27(4): 2431-2432.

Loh, K.H., Shao, K.T., Chen, H.M., Chen, C.H., Then, A.Y.H., Chong, V.C., Loo, P.L., Shen, K.N. & Hsiao, C.D. 2016b. Next generation sequencing yields the complete mitochondrial genome of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae). Mitochondrial DNA Part A, DNA Mapping, Sequencing and Analysis 27(6): 4230-4231.

Loh, K.H., Shao, K.T., Chen, C.H., Chen, H.M., Then, A.Y.H., Loo, P.L., Lim, P.E., Chong, V.C., Shen, K.N. & Hsiao, C.D. 2016c. Complete mitochondrial genome of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae). Mitochondrial DNA Part A, DNA Mapping, Sequencing and Analysis 27(4): 2651-2652.

Ojala, D., Montoya, J. & Attardi, G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature 290: 470-474.

Peninal, S., Subramanian, J., Elavarasi, A. & Kalaiselvam, M. 2017. Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters. Genomics Data 11: 81-84.

Reece, J.S., Bowen, B.W., Smith, D.G. & Larson, A. 2010. Molecular phylogenetics of moray eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean. Molecular Phylogenetics and Evolution 57: 829-835.

Schattner, P., Brooks, A.N. & Lowe, T.M. 2005. The tRNAscan- SE, snoscan and snoGPS servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research 33: W686-W689.

Smith, D.G. 2012. Checklist of the moray eels of the World (Teleostei: Anguilliformes: Muraenidae). Zootaxa 3474: 1-64.

Smith, D.G. & Böhlke, E.B. 1997. A review of the Indo-Pacific banded morays of the Gymnothorax reticularis group, with descriptions of three new species (Pisces, Anguilliformes, Muraenidae). Proceedings of the Academy of Natural Sciences of Philadelphia 148: 177-188.

Tang, K.L. & Fielitz, C. 2013. Phylogeny of moray eels (Anguilliformes: Muraenidae), with a revised classification of true eels (Teleostei: Elopomorpha: Anguilliformes). Mitochondrial DNA Part A, DNA Mapping, Sequencing, and Analysis 42: 55-66.

Tawa, A. & Mochioka, N. 2009. Identification of aquarium-raised muraenid leptocephali, Gymnothorax minor. Ichthyological Research 56: 340-345.

Tsukamoto, K., Watanabe, S., Kuroki, M., Aoyama, J. & Miller, M.J. 2014. Freshwater habitat use by a moray eel species, Gymnothorax polyuranodon, in Fiji shown by otolith microchemistry. Environmental Biology of Fishes 97: 1377- 1385.

White, P.S. & Densmore, L.D. 1992. Mitochondrial DNA isolation. In Molecular Genetic Analysis of Populations: A Practical Approach, edited by Hoelzel, A.R. Oxford: IRL Press, Oxford University Press. pp. 29-58.

Yong, H.S., Song, S.L., Lim, P.E., Chan, K.G., Chow, W.L. & Eamsobhana, P. 2015a. Complete mitochondrial genome of Bactrocera arecae (Insecta: Tephritidae) by next-generation sequencing and molecular phylogeny of Dacini tribe. Scientific Reports 5: 15155.

Yong, H.S., Song, S.L., Eamsobhana, P., Goh, S.Y., Lim, P.E., Chow, W.L., Chan, K.G. & Elizabeth, A.S. 2015b. Mitochondrial genome supports sibling species of Angiostrongylus costaricensis (Nematoda: Angiostrongylidae). PLoS ONE 10: e0134581.

Yoshida, T. 2013. Gymnothorax minor. In Fishes of northern Gulf of Thailand, edited by Yoshida, T., Motomura, H., Musikasinthorn, P. & Matsuura, K. National Museum of Nature and Science, Tsukuba; Research Institute for Humanity and Nature; Kagoshima: Kagoshima University Museum, Kyoto. p. 20.

 

*Corresponding author; email: khloh@um.edu.my